Dietary intake, Nutritional status, and Health outcomes among Vegan, Vegetarian and Omnivore families: results from the observational study
Statistical report - data wrangling and exploration
Authors and affiliations
Marina Heniková1,2, Anna Ouřadová1, Eliška Selinger1,3, Filip Tichanek4, Petra Polakovičová4, Dana Hrnčířová2, Pavel Dlouhý2, Martin Světnička5, Eva El-Lababidi5, Jana Potočková1, Tilman Kühn6, Monika Cahová4, Jan Gojda1
1 Department of Internal Medicine, Kralovske Vinohrady University Hospital and Third Faculty of Medicine, Charles University, Prague, Czech Republic.
2 Department of Hygiene, Third Faculty of Medicine, Charles University, Prague, Czech Republic.
3 National Health Institute, Prague, Czech Republic.
4 Institute for Clinical and Experimental Medicine, Prague, Czech Republic.
5 Department of Pediatrics, Kralovske Vinohrady University Hospital and Third Faculty of Medicine, Charles University, Prague, Czech Republic.
6 Department of Epidemiology, MedUni, Vienna, Austria.
This is a statistical report of the study currenlty under review in the Communications Medicine journal.
When using this code or data, cite the original publication:
TO BE ADDED
BibTex citation for the original publication:
TO BE ADDED
Original GitHub repository: https://github.com/filip-tichanek/kompas_clinical
Statistical reports can be found on the reports hub.
Data analysis is described in detail in the statistical methods report.
1 Introduction
This project is designed to evaluate and compare clinical outcomes across three distinct dietary strategy groups:
- Vegans
- Vegetarians
- Omnivores
The dataset includes both adults and children, with data clustered within families.
1.1 Main Questions
The study addresses the following key questions:
Q1. Do clinical outcomes vary significantly across different diet strategies?
Q2. Beyond diet group, which factors (e.g., sex, age, breastfeeding status for children, or supplementation when applicable) most strongly influence clinical outcomes? How correlated (“clustered”) are these characteristics within the same family?
Q3. Could the clinical characteristics effectively discriminate between different diet groups?
1.2 Statistical Methods
For full methodological details, see this report. In brief:
Robust linear mixed-effects models (rLME) were used to estimate adjusted differences between diet groups (Q1) and assess the importance of other variables (Q2), including how much clinical characteristics tend to cluster within families. Covariates included age, sex, breastfeeding status for children, and relevant supplementation factors where applicable.
Elastic net logistic regression was employed to answer Q3, evaluating whether clinical characteristics provide a strong overall signal distinguishing between diet groups, incorporating a predictive perspective.
All analyses were conducted separately for adults and children.
2 Analysis
2.1 Import initiation file
Open code
getwd()
## [1] "/home/ticf/GitRepo/ticf/368_MOCA_kompas_clinical"
setwd('/home/ticf/GitRepo/ticf/368_MOCA_kompas_clinical/')
source('r/368_initiation.R')2.2 Subject characteristics table
2.2.1 All children characteristics table
Comparison of clinical outcomes across diet groups in children
2.2.1.1 Overall
Open code
DatChar_child_all <- run(
dat_child_all_tosum %>%
select(-FAM, -ID) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')
) %>%
modify_caption(
"Supplementary Table 1. Children characteristics according to food preferences, all children"
) %>%
add_p() %>%
add_q(),
path = 'gitignore/run/DatChar_child_all', reuse = TRUE)
DatChar_child_allCharacteristic |
OM |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|---|
| aAGE | 3.04 (1.50, 5.51) | 3.85 (1.78, 5.84) | 2.17 (1.24, 3.57) | 0.016 | 0.063 |
| SEX | 0.9 | >0.9 | |||
| F | 24 (55%) | 18 (49%) | 31 (51%) | ||
| M | 20 (45%) | 19 (51%) | 30 (49%) | ||
| aBreastFeed_full | 6.00 (5.50, 6.00) | 6.00 (6.00, 7.00) | 6.00 (5.50, 6.00) | 0.002 | 0.013 |
| aBreastFeed_total | 10 (8, 14) | 18 (12, 21) | 15 (9, 19) | 0.006 | 0.030 |
| Unknown | 5 | 2 | 6 | ||
| aBreastFeed_full_stopped | 42 (95%) | 33 (89%) | 56 (92%) | 0.6 | 0.7 |
| aBreastFeed_total_stopped | 31 (79%) | 24 (69%) | 33 (60%) | 0.14 | 0.3 |
| Unknown | 5 | 2 | 6 | ||
| dev_delay | 1 (2.3%) | 1 (2.7%) | 1 (1.6%) | >0.9 | >0.9 |
| aMASS_Perc | 54 (30, 77) | 59 (29, 67) | 38 (14, 67) | 0.2 | 0.3 |
| aHEIGHT_Perc | 43 (23, 76) | 55 (33, 70) | 40 (11, 63) | 0.12 | 0.2 |
| aBMI_PERC | 49 (36, 70) | 50 (36, 60) | 52 (32, 69) | 0.8 | 0.8 |
| aM_per_H_PERC | 55 (32, 72) | 50 (33, 63) | 51 (35, 68) | 0.6 | 0.8 |
| aGLY | 4.40 (4.10, 4.62) | 4.61 (4.11, 4.76) | 4.42 (4.19, 4.60) | 0.9 | >0.9 |
| Unknown | 1 | 3 | 6 | ||
| aTC | 3.98 (3.31, 4.38) | 3.80 (3.32, 4.32) | 3.71 (3.23, 4.02) | 0.14 | 0.3 |
| Unknown | 1 | 3 | 6 | ||
| aHDL | 1.28 (0.93, 1.51) | 1.25 (1.04, 1.39) | 1.25 (1.03, 1.38) | >0.9 | >0.9 |
| Unknown | 1 | 3 | 6 | ||
| aLDL | 2.11 (1.74, 2.47) | 2.30 (1.85, 2.55) | 1.88 (1.58, 2.22) | 0.026 | 0.084 |
| Unknown | 1 | 3 | 6 | ||
| aTG | 1.03 (0.70, 1.25) | 0.71 (0.56, 0.96) | 1.01 (0.72, 1.40) | 0.016 | 0.063 |
| Unknown | 1 | 3 | 6 | ||
| aCa | 2.55 (2.48, 2.66) | 2.57 (2.45, 2.64) | 2.58 (2.49, 2.65) | 0.8 | 0.8 |
| Unknown | 1 | 3 | 5 | ||
| aP | 1.70 (1.56, 1.78) | 1.61 (1.49, 1.79) | 1.67 (1.55, 1.79) | 0.5 | 0.7 |
| Unknown | 1 | 3 | 5 | ||
| aMg | 0.83 (0.79, 0.88) | 0.85 (0.81, 0.91) | 0.87 (0.83, 0.92) | 0.023 | 0.076 |
| Unknown | 1 | 3 | 5 | ||
| aSe | 0.79 (0.71, 0.95) | 0.68 (0.60, 0.91) | 0.76 (0.53, 0.94) | 0.5 | 0.7 |
| Unknown | 1 | 4 | 6 | ||
| aZn | 11.70 (10.70, 13.40) | 11.30 (10.70, 12.50) | 10.60 (9.80, 12.20) | 0.085 | 0.2 |
| Unknown | 1 | 4 | 6 | ||
| aFE | 12 (8, 18) | 13 (6, 17) | 13 (9, 19) | 0.8 | 0.8 |
| Unknown | 1 | 3 | 5 | ||
| aVKFE | 75 (68, 79) | 73 (64, 77) | 70 (65, 76) | 0.12 | 0.2 |
| Unknown | 1 | 3 | 6 | ||
| aFERR | 19 (11, 24) | 15 (12, 20) | 14 (9, 17) | 0.039 | 0.11 |
| Unknown | 1 | 3 | 5 | ||
| aTRF | 2.96 (2.70, 3.15) | 2.89 (2.52, 3.04) | 2.75 (2.56, 3.00) | 0.10 | 0.2 |
| Unknown | 1 | 3 | 5 | ||
| aSATTRF | 16 (12, 23) | 18 (10, 27) | 19 (11, 26) | 0.6 | 0.7 |
| Unknown | 1 | 3 | 5 | ||
| aTRFINDEX | 1.37 (1.04, 1.73) | 1.38 (1.06, 1.54) | 1.40 (1.17, 1.79) | 0.3 | 0.5 |
| Unknown | 1 | 3 | 5 | ||
| aSTRF | 1.71 (1.44, 1.83) | 1.61 (1.39, 1.74) | 1.62 (1.44, 1.87) | 0.5 | 0.7 |
| Unknown | 1 | 3 | 5 | ||
| aHGB | 123 (113, 127) | 124 (117, 133) | 120 (115, 126) | 0.15 | 0.3 |
| Unknown | 3 | 4 | 7 | ||
| aMCV | 78.7 (75.1, 80.6) | 78.2 (76.7, 80.3) | 80.3 (78.4, 82.0) | 0.015 | 0.063 |
| Unknown | 3 | 4 | 7 | ||
| aPTH | 2.50 (1.70, 3.80) | 2.80 (1.90, 3.30) | 2.85 (2.20, 3.70) | 0.13 | 0.3 |
| Unknown | 1 | 4 | 5 | ||
| aCros | 1.22 (0.94, 1.41) | 1.24 (1.08, 1.41) | 1.24 (1.13, 1.43) | 0.5 | 0.7 |
| Unknown | 1 | 4 | 6 | ||
| aP1NP | 555 (433, 920) | 580 (447, 879) | 669 (562, 1,128) | 0.019 | 0.067 |
| Unknown | 1 | 4 | 6 | ||
| aUI | 169 (140, 248) | 136 (85, 242) | 99 (67, 160) | 0.002 | 0.013 |
| Unknown | 12 | 6 | 12 | ||
| aUREA | 4.50 (3.70, 5.60) | 4.25 (3.60, 5.10) | 3.95 (2.95, 4.65) | 0.016 | 0.063 |
| Unknown | 1 | 3 | 5 | ||
| aCREA | 27 (21, 33) | 27 (21, 34) | 23 (19, 29) | 0.017 | 0.063 |
| Unknown | 1 | 3 | 5 | ||
| aUA | 222 (198, 266) | 228 (205, 249) | 223 (188, 258) | 0.7 | 0.8 |
| Unknown | 1 | 3 | 5 | ||
| aVIT_AKTB12 | 94 (75, 125) | 91 (66, 122) | 143 (95, 217) | <0.001 | 0.002 |
| Unknown | 1 | 4 | 6 | ||
| aHCY | 8.90 (7.90, 10.40) | 8.35 (6.90, 10.40) | 7.35 (6.00, 8.80) | <0.001 | 0.004 |
| Unknown | 1 | 11 | 11 | ||
| aMMA | 229 (174, 307) | 202 (153, 409) | 153 (129, 196) | <0.001 | <0.001 |
| Unknown | 5 | 4 | 10 | ||
| aVIT_D | 75 (61, 96) | 87 (72, 111) | 99 (78, 118) | <0.001 | 0.007 |
| Unknown | 1 | 3 | 5 | ||
| aFOLAT | 13.2 (10.0, 16.9) | 17.9 (15.9, 19.5) | 18.0 (14.4, 22.1) | <0.001 | <0.001 |
| Unknown | 1 | 3 | 6 | ||
| aIGF1 | 107 (69, 156) | 126 (64, 180) | 81 (57, 116) | 0.038 | 0.11 |
| Unknown | 2 | 6 | 12 | ||
| aAL_child | 9 (20%) | 5 (14%) | 3 (4.9%) | 0.048 | 0.12 |
| aSUP_VEG1 | 0 (0%) | 4 (11%) | 3 (4.9%) | 0.065 | 0.2 |
| aSup_B12 | 0 (0%) | 25 (68%) | 46 (75%) | <0.001 | <0.001 |
| aSUP_FOL | 2 (4.5%) | 1 (2.7%) | 2 (3.3%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 0 (0%) | 2 (3.3%) | 0.5 | 0.7 |
| aSUP_vitB1 | 0 (0%) | 2 (5.4%) | 3 (4.9%) | 0.3 | 0.5 |
| aSUP_vit.B5 | 0 (0%) | 2 (5.4%) | 3 (4.9%) | 0.3 | 0.5 |
| aSUP_D | 21 (48%) | 33 (89%) | 48 (79%) | <0.001 | <0.001 |
| aSUP_Mg | 0 (0%) | 4 (11%) | 3 (4.9%) | 0.065 | 0.2 |
| aSUP_Zn | 0 (0%) | 0 (0%) | 5 (8.2%) | 0.043 | 0.12 |
| aSUP_Se | 0 (0%) | 0 (0%) | 3 (4.9%) | 0.3 | 0.4 |
| aSUP_Ca | 0 (0%) | 2 (5.4%) | 3 (4.9%) | 0.3 | 0.5 |
| aSUP_Fe | 2 (4.5%) | 4 (11%) | 4 (6.6%) | 0.6 | 0.7 |
| aSUP_Iod | 0 (0%) | 3 (8.1%) | 6 (9.8%) | 0.076 | 0.2 |
| aSUP_Ѡ3 | 5 (11%) | 13 (35%) | 39 (64%) | <0.001 | <0.001 |
| aSUP_CHLO | 0 (0%) | 3 (8.1%) | 0 (0%) | 0.017 | 0.063 |
| aSUP_ALG | |||||
| 0 | 44 (100%) | 37 (100%) | 61 (100%) | ||
| aSUP_GB | 0 (0%) | 1 (2.7%) | 0 (0%) | 0.3 | 0.4 |
| aSUP_FORT | 0 (0%) | 1 (2.7%) | 0 (0%) | 0.3 | 0.4 |
| aSUP_PROB | 3 (6.8%) | 6 (16%) | 0 (0%) | 0.003 | 0.018 |
| aSUP_OTH | 14 (32%) | 9 (24%) | 7 (11%) | 0.036 | 0.11 |
| aUr_Krea | 5.1 (2.4, 5.9) | 3.9 (2.1, 6.6) | 2.9 (1.3, 5.3) | 0.051 | 0.13 |
| Unknown | 9 | 1 | 8 | ||
| aUr_Ca | 1.15 (0.49, 2.25) | 1.14 (0.44, 3.10) | 0.65 (0.27, 1.86) | 0.2 | 0.3 |
| Unknown | 9 | 1 | 8 | ||
| aCa_per_Krea | 0.25 (0.11, 0.50) | 0.38 (0.12, 0.81) | 0.28 (0.19, 0.61) | 0.5 | 0.6 |
| Unknown | 9 | 1 | 8 | ||
| aI_per_Krea | 344 (205, 614) | 325 (148, 669) | 361 (199, 503) | 0.9 | >0.9 |
| Unknown | 12 | 6 | 13 | ||
| aP_per_Krea | 4.20 (2.77, 6.10) | 3.51 (1.68, 4.49) | 2.50 (1.44, 3.92) | <0.001 | 0.004 |
| Unknown | 9 | 1 | 8 | ||
| aBiW | 3,310 (3,030, 3,650) | 3,370 (3,090, 3,600) | 3,500 (3,050, 3,690) | >0.9 | >0.9 |
| Unknown | 0 | 0 | 2 | ||
| aBREAKS | 1 (2.3%) | 0 (0%) | 4 (6.6%) | 0.3 | 0.4 |
| 1
Median (Q1, Q3); n (%) |
|||||
| 2
Kruskal-Wallis rank sum test; Pearson’s Chi-squared test; Fisher’s exact test |
|||||
| 3
False discovery rate correction for multiple testing |
|||||
Open code
DatChar_child_all_df <- DatChar_child_all$table_body %>%
as_tibble()2.2.1.2 OM vs VG
Open code
DatChar_child_all_OM_VG <- run(
dat_child_all_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'OM' | GRP == 'VG') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("OM vs VG, all children") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_all_OM_VG', reuse = TRUE)
DatChar_child_all_OM_VGCharacteristic |
OM |
VG |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 3.04 (1.50, 5.51) | 3.85 (1.78, 5.84) | 0.5 | 0.8 |
| SEX | 0.6 | 0.8 | ||
| F | 24 (55%) | 18 (49%) | ||
| M | 20 (45%) | 19 (51%) | ||
| aBreastFeed_full | 6.00 (5.50, 6.00) | 6.00 (6.00, 7.00) | 0.002 | 0.022 |
| aBreastFeed_total | 10 (8, 14) | 18 (12, 21) | 0.001 | 0.022 |
| Unknown | 5 | 2 | ||
| aBreastFeed_full_stopped | 42 (95%) | 33 (89%) | 0.4 | 0.8 |
| aBreastFeed_total_stopped | 31 (79%) | 24 (69%) | 0.3 | 0.8 |
| Unknown | 5 | 2 | ||
| dev_delay | 1 (2.3%) | 1 (2.7%) | >0.9 | >0.9 |
| aMASS_Perc | 54 (30, 77) | 59 (29, 67) | 0.7 | 0.8 |
| aHEIGHT_Perc | 43 (23, 76) | 55 (33, 70) | 0.7 | 0.9 |
| aBMI_PERC | 49 (36, 70) | 50 (36, 60) | 0.5 | 0.8 |
| aM_per_H_PERC | 55 (32, 72) | 50 (33, 63) | 0.4 | 0.8 |
| aGLY | 4.40 (4.10, 4.62) | 4.61 (4.11, 4.76) | 0.6 | 0.8 |
| Unknown | 1 | 3 | ||
| aTC | 3.98 (3.31, 4.38) | 3.80 (3.32, 4.32) | 0.5 | 0.8 |
| Unknown | 1 | 3 | ||
| aHDL | 1.28 (0.93, 1.51) | 1.25 (1.04, 1.39) | 0.8 | >0.9 |
| Unknown | 1 | 3 | ||
| aLDL | 2.11 (1.74, 2.47) | 2.30 (1.85, 2.55) | 0.5 | 0.8 |
| Unknown | 1 | 3 | ||
| aTG | 1.03 (0.70, 1.25) | 0.71 (0.56, 0.96) | 0.018 | 0.2 |
| Unknown | 1 | 3 | ||
| aCa | 2.55 (2.48, 2.66) | 2.57 (2.45, 2.64) | 0.8 | >0.9 |
| Unknown | 1 | 3 | ||
| aP | 1.70 (1.56, 1.78) | 1.61 (1.49, 1.79) | 0.3 | 0.8 |
| Unknown | 1 | 3 | ||
| aMg | 0.83 (0.79, 0.88) | 0.85 (0.81, 0.91) | 0.2 | 0.8 |
| Unknown | 1 | 3 | ||
| aSe | 0.79 (0.71, 0.95) | 0.68 (0.60, 0.91) | 0.3 | 0.8 |
| Unknown | 1 | 4 | ||
| aZn | 11.70 (10.70, 13.40) | 11.30 (10.70, 12.50) | 0.5 | 0.8 |
| Unknown | 1 | 4 | ||
| aFE | 12 (8, 18) | 13 (6, 17) | 0.9 | >0.9 |
| Unknown | 1 | 3 | ||
| aVKFE | 75 (68, 79) | 73 (64, 77) | 0.4 | 0.8 |
| Unknown | 1 | 3 | ||
| aFERR | 19 (11, 24) | 15 (12, 20) | 0.6 | 0.8 |
| Unknown | 1 | 3 | ||
| aTRF | 2.96 (2.70, 3.15) | 2.89 (2.52, 3.04) | 0.3 | 0.8 |
| Unknown | 1 | 3 | ||
| aSATTRF | 16 (12, 23) | 18 (10, 27) | 0.8 | >0.9 |
| Unknown | 1 | 3 | ||
| aTRFINDEX | 1.37 (1.04, 1.73) | 1.38 (1.06, 1.54) | >0.9 | >0.9 |
| Unknown | 1 | 3 | ||
| aSTRF | 1.71 (1.44, 1.83) | 1.61 (1.39, 1.74) | 0.3 | 0.8 |
| Unknown | 1 | 3 | ||
| aHGB | 123 (113, 127) | 124 (117, 133) | 0.3 | 0.8 |
| Unknown | 3 | 4 | ||
| aMCV | 78.7 (75.1, 80.6) | 78.2 (76.7, 80.3) | >0.9 | >0.9 |
| Unknown | 3 | 4 | ||
| aPTH | 2.50 (1.70, 3.80) | 2.80 (1.90, 3.30) | >0.9 | >0.9 |
| Unknown | 1 | 4 | ||
| aCros | 1.22 (0.94, 1.41) | 1.24 (1.08, 1.41) | 0.4 | 0.8 |
| Unknown | 1 | 4 | ||
| aP1NP | 555 (433, 920) | 580 (447, 879) | 0.8 | >0.9 |
| Unknown | 1 | 4 | ||
| aUI | 169 (140, 248) | 136 (85, 242) | 0.2 | 0.8 |
| Unknown | 12 | 6 | ||
| aUREA | 4.50 (3.70, 5.60) | 4.25 (3.60, 5.10) | 0.3 | 0.8 |
| Unknown | 1 | 3 | ||
| aCREA | 27 (21, 33) | 27 (21, 34) | 0.8 | >0.9 |
| Unknown | 1 | 3 | ||
| aUA | 222 (198, 266) | 228 (205, 249) | 0.8 | >0.9 |
| Unknown | 1 | 3 | ||
| aVIT_AKTB12 | 94 (75, 125) | 91 (66, 122) | 0.6 | 0.8 |
| Unknown | 1 | 4 | ||
| aHCY | 8.90 (7.90, 10.40) | 8.35 (6.90, 10.40) | 0.3 | 0.8 |
| Unknown | 1 | 11 | ||
| aMMA | 229 (174, 307) | 202 (153, 409) | 0.3 | 0.8 |
| Unknown | 5 | 4 | ||
| aVIT_D | 75 (61, 96) | 87 (72, 111) | 0.022 | 0.2 |
| Unknown | 1 | 3 | ||
| aFOLAT | 13.2 (10.0, 16.9) | 17.9 (15.9, 19.5) | <0.001 | <0.001 |
| Unknown | 1 | 3 | ||
| aIGF1 | 107 (69, 156) | 126 (64, 180) | 0.5 | 0.8 |
| Unknown | 2 | 6 | ||
| aAL_child | 9 (20%) | 5 (14%) | 0.4 | 0.8 |
| aSUP_VEG1 | 0 (0%) | 4 (11%) | 0.040 | 0.3 |
| aSup_B12 | 0 (0%) | 25 (68%) | <0.001 | <0.001 |
| aSUP_FOL | 2 (4.5%) | 1 (2.7%) | >0.9 | >0.9 |
| aSUP_vitA | ||||
| 0 | 44 (100%) | 37 (100%) | ||
| aSUP_vitB1 | 0 (0%) | 2 (5.4%) | 0.2 | 0.8 |
| aSUP_vit.B5 | 0 (0%) | 2 (5.4%) | 0.2 | 0.8 |
| aSUP_D | 21 (48%) | 33 (89%) | <0.001 | 0.002 |
| aSUP_Mg | 0 (0%) | 4 (11%) | 0.040 | 0.3 |
| aSUP_Zn | ||||
| 0 | 44 (100%) | 37 (100%) | ||
| aSUP_Se | ||||
| 0 | 44 (100%) | 37 (100%) | ||
| aSUP_Ca | 0 (0%) | 2 (5.4%) | 0.2 | 0.8 |
| aSUP_Fe | 2 (4.5%) | 4 (11%) | 0.4 | 0.8 |
| aSUP_Iod | 0 (0%) | 3 (8.1%) | 0.091 | 0.5 |
| aSUP_Ѡ3 | 5 (11%) | 13 (35%) | 0.010 | 0.12 |
| aSUP_CHLO | 0 (0%) | 3 (8.1%) | 0.091 | 0.5 |
| aSUP_ALG | ||||
| 0 | 44 (100%) | 37 (100%) | ||
| aSUP_GB | 0 (0%) | 1 (2.7%) | 0.5 | 0.8 |
| aSUP_FORT | 0 (0%) | 1 (2.7%) | 0.5 | 0.8 |
| aSUP_PROB | 3 (6.8%) | 6 (16%) | 0.3 | 0.8 |
| aSUP_OTH | 14 (32%) | 9 (24%) | 0.5 | 0.8 |
| aUr_Krea | 5.1 (2.4, 5.9) | 3.9 (2.1, 6.6) | 0.5 | 0.8 |
| Unknown | 9 | 1 | ||
| aUr_Ca | 1.15 (0.49, 2.25) | 1.14 (0.44, 3.10) | 0.6 | 0.8 |
| Unknown | 9 | 1 | ||
| aCa_per_Krea | 0.25 (0.11, 0.50) | 0.38 (0.12, 0.81) | 0.2 | 0.8 |
| Unknown | 9 | 1 | ||
| aI_per_Krea | 344 (205, 614) | 325 (148, 669) | 0.6 | 0.8 |
| Unknown | 12 | 6 | ||
| aP_per_Krea | 4.20 (2.77, 6.10) | 3.51 (1.68, 4.49) | 0.046 | 0.3 |
| Unknown | 9 | 1 | ||
| aBiW | 3,310 (3,030, 3,650) | 3,370 (3,090, 3,600) | >0.9 | >0.9 |
| aBREAKS | 1 (2.3%) | 0 (0%) | >0.9 | >0.9 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test; Wilcoxon rank sum exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.1.3 OM vs VG
Open code
DatChar_child_all_OM_VN <- run(
dat_child_all_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'OM' | GRP == 'VN') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("OM vs VN, only children >3 year all included") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_all_OM_VN', reuse=TRUE)
DatChar_child_all_OM_VNCharacteristic |
OM |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 3.04 (1.50, 5.51) | 2.17 (1.24, 3.57) | 0.051 | 0.13 |
| SEX | 0.7 | 0.8 | ||
| F | 24 (55%) | 31 (51%) | ||
| M | 20 (45%) | 30 (49%) | ||
| aBreastFeed_full | 6.00 (5.50, 6.00) | 6.00 (5.50, 6.00) | >0.9 | >0.9 |
| aBreastFeed_total | 10 (8, 14) | 15 (9, 19) | 0.047 | 0.13 |
| Unknown | 5 | 6 | ||
| aBreastFeed_full_stopped | 42 (95%) | 56 (92%) | 0.7 | 0.8 |
| aBreastFeed_total_stopped | 31 (79%) | 33 (60%) | 0.046 | 0.13 |
| Unknown | 5 | 6 | ||
| dev_delay | 1 (2.3%) | 1 (1.6%) | >0.9 | >0.9 |
| aMASS_Perc | 54 (30, 77) | 38 (14, 67) | 0.10 | 0.2 |
| aHEIGHT_Perc | 43 (23, 76) | 40 (11, 63) | 0.2 | 0.3 |
| aBMI_PERC | 49 (36, 70) | 52 (32, 69) | 0.5 | 0.7 |
| aM_per_H_PERC | 55 (32, 72) | 51 (35, 68) | 0.5 | 0.6 |
| aGLY | 4.40 (4.10, 4.62) | 4.42 (4.19, 4.60) | 0.8 | >0.9 |
| Unknown | 1 | 6 | ||
| aTC | 3.98 (3.31, 4.38) | 3.71 (3.23, 4.02) | 0.048 | 0.13 |
| Unknown | 1 | 6 | ||
| aHDL | 1.28 (0.93, 1.51) | 1.25 (1.03, 1.38) | >0.9 | >0.9 |
| Unknown | 1 | 6 | ||
| aLDL | 2.11 (1.74, 2.47) | 1.88 (1.58, 2.22) | 0.073 | 0.2 |
| Unknown | 1 | 6 | ||
| aTG | 1.03 (0.70, 1.25) | 1.01 (0.72, 1.40) | 0.8 | >0.9 |
| Unknown | 1 | 6 | ||
| aCa | 2.55 (2.48, 2.66) | 2.58 (2.49, 2.65) | 0.7 | 0.8 |
| Unknown | 1 | 5 | ||
| aP | 1.70 (1.56, 1.78) | 1.67 (1.55, 1.79) | 0.7 | 0.8 |
| Unknown | 1 | 5 | ||
| aMg | 0.83 (0.79, 0.88) | 0.87 (0.83, 0.92) | 0.006 | 0.034 |
| Unknown | 1 | 5 | ||
| aSe | 0.79 (0.71, 0.95) | 0.76 (0.53, 0.94) | 0.4 | 0.6 |
| Unknown | 1 | 6 | ||
| aZn | 11.70 (10.70, 13.40) | 10.60 (9.80, 12.20) | 0.049 | 0.13 |
| Unknown | 1 | 6 | ||
| aFE | 12 (8, 18) | 13 (9, 19) | 0.5 | 0.7 |
| Unknown | 1 | 5 | ||
| aVKFE | 75 (68, 79) | 70 (65, 76) | 0.037 | 0.12 |
| Unknown | 1 | 6 | ||
| aFERR | 19 (11, 24) | 14 (9, 17) | 0.018 | 0.071 |
| Unknown | 1 | 5 | ||
| aTRF | 2.96 (2.70, 3.15) | 2.75 (2.56, 3.00) | 0.029 | 0.10 |
| Unknown | 1 | 5 | ||
| aSATTRF | 16 (12, 23) | 19 (11, 26) | 0.3 | 0.5 |
| Unknown | 1 | 5 | ||
| aTRFINDEX | 1.37 (1.04, 1.73) | 1.40 (1.17, 1.79) | 0.2 | 0.4 |
| Unknown | 1 | 5 | ||
| aSTRF | 1.71 (1.44, 1.83) | 1.62 (1.44, 1.87) | >0.9 | >0.9 |
| Unknown | 1 | 5 | ||
| aHGB | 123 (113, 127) | 120 (115, 126) | 0.4 | 0.6 |
| Unknown | 3 | 7 | ||
| aMCV | 78.7 (75.1, 80.6) | 80.3 (78.4, 82.0) | 0.015 | 0.064 |
| Unknown | 3 | 7 | ||
| aPTH | 2.50 (1.70, 3.80) | 2.85 (2.20, 3.70) | 0.10 | 0.2 |
| Unknown | 1 | 5 | ||
| aCros | 1.22 (0.94, 1.41) | 1.24 (1.13, 1.43) | 0.2 | 0.4 |
| Unknown | 1 | 6 | ||
| aP1NP | 555 (433, 920) | 669 (562, 1,128) | 0.010 | 0.049 |
| Unknown | 1 | 6 | ||
| aUI | 169 (140, 248) | 99 (67, 160) | <0.001 | 0.003 |
| Unknown | 12 | 12 | ||
| aUREA | 4.50 (3.70, 5.60) | 3.95 (2.95, 4.65) | 0.004 | 0.025 |
| Unknown | 1 | 5 | ||
| aCREA | 27 (21, 33) | 23 (19, 29) | 0.024 | 0.084 |
| Unknown | 1 | 5 | ||
| aUA | 222 (198, 266) | 223 (188, 258) | 0.5 | 0.7 |
| Unknown | 1 | 5 | ||
| aVIT_AKTB12 | 94 (75, 125) | 143 (95, 217) | <0.001 | 0.002 |
| Unknown | 1 | 6 | ||
| aHCY | 8.90 (7.90, 10.40) | 7.35 (6.00, 8.80) | <0.001 | 0.001 |
| Unknown | 1 | 11 | ||
| aMMA | 229 (174, 307) | 153 (129, 196) | <0.001 | <0.001 |
| Unknown | 5 | 10 | ||
| aVIT_D | 75 (61, 96) | 99 (78, 118) | <0.001 | 0.002 |
| Unknown | 1 | 5 | ||
| aFOLAT | 13.2 (10.0, 16.9) | 18.0 (14.4, 22.1) | <0.001 | <0.001 |
| Unknown | 1 | 6 | ||
| aIGF1 | 107 (69, 156) | 81 (57, 116) | 0.081 | 0.2 |
| Unknown | 2 | 12 | ||
| aAL_child | 9 (20%) | 3 (4.9%) | 0.014 | 0.061 |
| aSUP_VEG1 | 0 (0%) | 3 (4.9%) | 0.3 | 0.4 |
| aSup_B12 | 0 (0%) | 46 (75%) | <0.001 | <0.001 |
| aSUP_FOL | 2 (4.5%) | 2 (3.3%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 2 (3.3%) | 0.5 | 0.7 |
| aSUP_vitB1 | 0 (0%) | 3 (4.9%) | 0.3 | 0.4 |
| aSUP_vit.B5 | 0 (0%) | 3 (4.9%) | 0.3 | 0.4 |
| aSUP_D | 21 (48%) | 48 (79%) | <0.001 | 0.007 |
| aSUP_Mg | 0 (0%) | 3 (4.9%) | 0.3 | 0.4 |
| aSUP_Zn | 0 (0%) | 5 (8.2%) | 0.073 | 0.2 |
| aSUP_Se | 0 (0%) | 3 (4.9%) | 0.3 | 0.4 |
| aSUP_Ca | 0 (0%) | 3 (4.9%) | 0.3 | 0.4 |
| aSUP_Fe | 2 (4.5%) | 4 (6.6%) | >0.9 | >0.9 |
| aSUP_Iod | 0 (0%) | 6 (9.8%) | 0.039 | 0.12 |
| aSUP_Ѡ3 | 5 (11%) | 39 (64%) | <0.001 | <0.001 |
| aSUP_CHLO | ||||
| 0 | 44 (100%) | 61 (100%) | ||
| aSUP_ALG | ||||
| 0 | 44 (100%) | 61 (100%) | ||
| aSUP_GB | ||||
| 0 | 44 (100%) | 61 (100%) | ||
| aSUP_FORT | ||||
| 0 | 44 (100%) | 61 (100%) | ||
| aSUP_PROB | 3 (6.8%) | 0 (0%) | 0.071 | 0.2 |
| aSUP_OTH | 14 (32%) | 7 (11%) | 0.010 | 0.049 |
| aUr_Krea | 5.1 (2.4, 5.9) | 2.9 (1.3, 5.3) | 0.024 | 0.084 |
| Unknown | 9 | 8 | ||
| aUr_Ca | 1.15 (0.49, 2.25) | 0.65 (0.27, 1.86) | 0.3 | 0.4 |
| Unknown | 9 | 8 | ||
| aCa_per_Krea | 0.25 (0.11, 0.50) | 0.28 (0.19, 0.61) | 0.4 | 0.6 |
| Unknown | 9 | 8 | ||
| aI_per_Krea | 344 (205, 614) | 361 (199, 503) | 0.7 | 0.8 |
| Unknown | 12 | 13 | ||
| aP_per_Krea | 4.20 (2.77, 6.10) | 2.50 (1.44, 3.92) | <0.001 | 0.001 |
| Unknown | 9 | 8 | ||
| aBiW | 3,310 (3,030, 3,650) | 3,500 (3,050, 3,690) | >0.9 | >0.9 |
| Unknown | 0 | 2 | ||
| aBREAKS | 1 (2.3%) | 4 (6.6%) | 0.4 | 0.6 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.1.4 VG vs VN
Open code
DatChar_child_all_VG_VN <- run(
dat_child_all_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'VG' | GRP == 'VN') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("VG vs VN, only children >3 year all included") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_all_VG_VN', reuse=TRUE)
DatChar_child_all_VG_VNCharacteristic |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 3.85 (1.78, 5.84) | 2.17 (1.24, 3.57) | 0.007 | 0.070 |
| SEX | 0.8 | >0.9 | ||
| F | 18 (49%) | 31 (51%) | ||
| M | 19 (51%) | 30 (49%) | ||
| aBreastFeed_full | 6.00 (6.00, 7.00) | 6.00 (5.50, 6.00) | 0.002 | 0.046 |
| aBreastFeed_total | 18 (12, 21) | 15 (9, 19) | 0.13 | 0.4 |
| Unknown | 2 | 6 | ||
| aBreastFeed_full_stopped | 33 (89%) | 56 (92%) | 0.7 | >0.9 |
| aBreastFeed_total_stopped | 24 (69%) | 33 (60%) | 0.4 | 0.6 |
| Unknown | 2 | 6 | ||
| dev_delay | 1 (2.7%) | 1 (1.6%) | >0.9 | >0.9 |
| aMASS_Perc | 59 (29, 67) | 38 (14, 67) | 0.2 | 0.5 |
| aHEIGHT_Perc | 55 (33, 70) | 40 (11, 63) | 0.045 | 0.2 |
| aBMI_PERC | 50 (36, 60) | 52 (32, 69) | 0.9 | >0.9 |
| aM_per_H_PERC | 50 (33, 63) | 51 (35, 68) | 0.8 | >0.9 |
| aGLY | 4.61 (4.11, 4.76) | 4.42 (4.19, 4.60) | 0.6 | 0.8 |
| Unknown | 3 | 6 | ||
| aTC | 3.80 (3.32, 4.32) | 3.71 (3.23, 4.02) | 0.3 | 0.6 |
| Unknown | 3 | 6 | ||
| aHDL | 1.25 (1.04, 1.39) | 1.25 (1.03, 1.38) | >0.9 | >0.9 |
| Unknown | 3 | 6 | ||
| aLDL | 2.30 (1.85, 2.55) | 1.88 (1.58, 2.22) | 0.009 | 0.081 |
| Unknown | 3 | 6 | ||
| aTG | 0.71 (0.56, 0.96) | 1.01 (0.72, 1.40) | 0.007 | 0.070 |
| Unknown | 3 | 6 | ||
| aCa | 2.57 (2.45, 2.64) | 2.58 (2.49, 2.65) | 0.4 | 0.7 |
| Unknown | 3 | 5 | ||
| aP | 1.61 (1.49, 1.79) | 1.67 (1.55, 1.79) | 0.4 | 0.6 |
| Unknown | 3 | 5 | ||
| aMg | 0.85 (0.81, 0.91) | 0.87 (0.83, 0.92) | 0.2 | 0.5 |
| Unknown | 3 | 5 | ||
| aSe | 0.68 (0.60, 0.91) | 0.76 (0.53, 0.94) | >0.9 | >0.9 |
| Unknown | 4 | 6 | ||
| aZn | 11.30 (10.70, 12.50) | 10.60 (9.80, 12.20) | 0.11 | 0.3 |
| Unknown | 4 | 6 | ||
| aFE | 13 (6, 17) | 13 (9, 19) | 0.6 | 0.8 |
| Unknown | 3 | 5 | ||
| aVKFE | 73 (64, 77) | 70 (65, 76) | 0.4 | 0.6 |
| Unknown | 3 | 6 | ||
| aFERR | 15 (12, 20) | 14 (9, 17) | 0.081 | 0.3 |
| Unknown | 3 | 5 | ||
| aTRF | 2.89 (2.52, 3.04) | 2.75 (2.56, 3.00) | 0.4 | 0.6 |
| Unknown | 3 | 5 | ||
| aSATTRF | 18 (10, 27) | 19 (11, 26) | 0.6 | 0.8 |
| Unknown | 3 | 5 | ||
| aTRFINDEX | 1.38 (1.06, 1.54) | 1.40 (1.17, 1.79) | 0.2 | 0.4 |
| Unknown | 3 | 5 | ||
| aSTRF | 1.61 (1.39, 1.74) | 1.62 (1.44, 1.87) | 0.4 | 0.6 |
| Unknown | 3 | 5 | ||
| aHGB | 124 (117, 133) | 120 (115, 126) | 0.050 | 0.2 |
| Unknown | 4 | 7 | ||
| aMCV | 78.2 (76.7, 80.3) | 80.3 (78.4, 82.0) | 0.016 | 0.10 |
| Unknown | 4 | 7 | ||
| aPTH | 2.80 (1.90, 3.30) | 2.85 (2.20, 3.70) | 0.087 | 0.3 |
| Unknown | 4 | 5 | ||
| aCros | 1.24 (1.08, 1.41) | 1.24 (1.13, 1.43) | >0.9 | >0.9 |
| Unknown | 4 | 6 | ||
| aP1NP | 580 (447, 879) | 669 (562, 1,128) | 0.038 | 0.2 |
| Unknown | 4 | 6 | ||
| aUI | 136 (85, 242) | 99 (67, 160) | 0.078 | 0.3 |
| Unknown | 6 | 12 | ||
| aUREA | 4.25 (3.60, 5.10) | 3.95 (2.95, 4.65) | 0.13 | 0.4 |
| Unknown | 3 | 5 | ||
| aCREA | 27 (21, 34) | 23 (19, 29) | 0.012 | 0.10 |
| Unknown | 3 | 5 | ||
| aUA | 228 (205, 249) | 223 (188, 258) | 0.5 | 0.8 |
| Unknown | 3 | 5 | ||
| aVIT_AKTB12 | 91 (66, 122) | 143 (95, 217) | <0.001 | 0.046 |
| Unknown | 4 | 6 | ||
| aHCY | 8.35 (6.90, 10.40) | 7.35 (6.00, 8.80) | 0.026 | 0.2 |
| Unknown | 11 | 11 | ||
| aMMA | 202 (153, 409) | 153 (129, 196) | 0.003 | 0.046 |
| Unknown | 4 | 10 | ||
| aVIT_D | 87 (72, 111) | 99 (78, 118) | 0.2 | 0.5 |
| Unknown | 3 | 5 | ||
| aFOLAT | 17.9 (15.9, 19.5) | 18.0 (14.4, 22.1) | 0.6 | 0.8 |
| Unknown | 3 | 6 | ||
| aIGF1 | 126 (64, 180) | 81 (57, 116) | 0.015 | 0.10 |
| Unknown | 6 | 12 | ||
| aAL_child | 5 (14%) | 3 (4.9%) | 0.15 | 0.4 |
| aSUP_VEG1 | 4 (11%) | 3 (4.9%) | 0.4 | 0.6 |
| aSup_B12 | 25 (68%) | 46 (75%) | 0.4 | 0.6 |
| aSUP_FOL | 1 (2.7%) | 2 (3.3%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 2 (3.3%) | 0.5 | 0.8 |
| aSUP_vitB1 | 2 (5.4%) | 3 (4.9%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 2 (5.4%) | 3 (4.9%) | >0.9 | >0.9 |
| aSUP_D | 33 (89%) | 48 (79%) | 0.2 | 0.4 |
| aSUP_Mg | 4 (11%) | 3 (4.9%) | 0.4 | 0.6 |
| aSUP_Zn | 0 (0%) | 5 (8.2%) | 0.2 | 0.4 |
| aSUP_Se | 0 (0%) | 3 (4.9%) | 0.3 | 0.6 |
| aSUP_Ca | 2 (5.4%) | 3 (4.9%) | >0.9 | >0.9 |
| aSUP_Fe | 4 (11%) | 4 (6.6%) | 0.5 | 0.7 |
| aSUP_Iod | 3 (8.1%) | 6 (9.8%) | >0.9 | >0.9 |
| aSUP_Ѡ3 | 13 (35%) | 39 (64%) | 0.006 | 0.070 |
| aSUP_CHLO | 3 (8.1%) | 0 (0%) | 0.051 | 0.2 |
| aSUP_ALG | ||||
| 0 | 37 (100%) | 61 (100%) | ||
| aSUP_GB | 1 (2.7%) | 0 (0%) | 0.4 | 0.6 |
| aSUP_FORT | 1 (2.7%) | 0 (0%) | 0.4 | 0.6 |
| aSUP_PROB | 6 (16%) | 0 (0%) | 0.002 | 0.046 |
| aSUP_OTH | 9 (24%) | 7 (11%) | 0.10 | 0.3 |
| aUr_Krea | 3.85 (2.10, 6.55) | 2.90 (1.30, 5.30) | 0.094 | 0.3 |
| Unknown | 1 | 8 | ||
| aUr_Ca | 1.14 (0.44, 3.10) | 0.65 (0.27, 1.86) | 0.082 | 0.3 |
| Unknown | 1 | 8 | ||
| aCa_per_Krea | 0.38 (0.12, 0.81) | 0.28 (0.19, 0.61) | 0.6 | 0.8 |
| Unknown | 1 | 8 | ||
| aI_per_Krea | 325 (148, 669) | 361 (199, 503) | >0.9 | >0.9 |
| Unknown | 6 | 13 | ||
| aP_per_Krea | 3.51 (1.68, 4.49) | 2.50 (1.44, 3.92) | 0.073 | 0.3 |
| Unknown | 1 | 8 | ||
| aBiW | 3,370 (3,090, 3,600) | 3,500 (3,050, 3,690) | 0.7 | >0.9 |
| Unknown | 0 | 2 | ||
| aBREAKS | 0 (0%) | 4 (6.6%) | 0.3 | 0.6 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test; Wilcoxon rank sum exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.2 Children >3 y.o. characteristics table
2.2.2.1 Overall
Open code
DatChar_child_old <- run(
dat_child_old_tosum %>%
select(-FAM, -ID) %>%
tbl_summary(
by='GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("Supplementary Table 2. Children characteristics according to food preferences, with only children >3 year old included") %>%
add_p() %>%
add_q(),
path = 'gitignore/run/DatChar_child_old', reuse=TRUE)
DatChar_child_oldCharacteristic |
OM |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|---|
| aAGE | 5.51 (4.27, 6.30) | 5.28 (4.40, 6.89) | 4.67 (3.57, 5.78) | 0.14 | 0.3 |
| SEX | 0.5 | 0.7 | |||
| F | 13 (59%) | 9 (41%) | 10 (48%) | ||
| M | 9 (41%) | 13 (59%) | 11 (52%) | ||
| aBreastFeed_full | 6.00 (5.00, 6.00) | 7.00 (6.00, 8.00) | 6.00 (6.00, 6.00) | <0.001 | 0.011 |
| aBreastFeed_total | 10 (8, 16) | 18 (15, 22) | 18 (12, 35) | 0.003 | 0.029 |
| Unknown | 3 | 0 | 2 | ||
| aBreastFeed_full_stopped | |||||
| 1 | 22 (100%) | 22 (100%) | 21 (100%) | ||
| aBreastFeed_total_stopped | 19 (100%) | 22 (100%) | 18 (95%) | 0.6 | 0.8 |
| Unknown | 3 | 0 | 2 | ||
| dev_delay | 1 (4.5%) | 1 (4.5%) | 1 (4.8%) | >0.9 | >0.9 |
| aMASS_Perc | 52 (28, 76) | 62 (27, 65) | 40 (27, 67) | 0.6 | 0.8 |
| aHEIGHT_Perc | 41 (18, 76) | 57 (37, 74) | 42 (11, 61) | 0.4 | 0.7 |
| aBMI_PERC | 46 (34, 63) | 46 (31, 58) | 43 (21, 68) | 0.9 | >0.9 |
| aM_per_H_PERC | 47 (29, 63) | 47 (32, 58) | 43 (17, 70) | 0.8 | >0.9 |
| aGLY | 4.28 (3.97, 4.74) | 4.26 (3.79, 4.72) | 4.33 (4.19, 4.56) | >0.9 | >0.9 |
| Unknown | 0 | 1 | 0 | ||
| aTC | 4.05 (3.60, 4.26) | 3.70 (3.19, 4.32) | 3.42 (3.20, 3.87) | 0.045 | 0.2 |
| Unknown | 0 | 1 | 0 | ||
| aHDL | 1.35 (1.03, 1.68) | 1.31 (1.10, 1.43) | 1.23 (1.12, 1.49) | 0.7 | 0.9 |
| Unknown | 0 | 1 | 0 | ||
| aLDL | 2.15 (1.83, 2.26) | 2.11 (1.79, 2.49) | 1.71 (1.56, 2.03) | 0.029 | 0.2 |
| Unknown | 0 | 1 | 0 | ||
| aTG | 0.89 (0.70, 1.22) | 0.62 (0.56, 0.92) | 0.93 (0.65, 1.10) | 0.2 | 0.3 |
| Unknown | 0 | 1 | 0 | ||
| aCa | 2.50 (2.44, 2.55) | 2.50 (2.45, 2.58) | 2.49 (2.47, 2.52) | >0.9 | >0.9 |
| Unknown | 0 | 1 | 0 | ||
| aP | 1.65 (1.48, 1.77) | 1.54 (1.44, 1.63) | 1.58 (1.43, 1.67) | 0.5 | 0.7 |
| Unknown | 0 | 1 | 0 | ||
| aMg | 0.82 (0.79, 0.85) | 0.83 (0.80, 0.87) | 0.86 (0.81, 0.89) | 0.090 | 0.3 |
| Unknown | 0 | 1 | 0 | ||
| aSe | 0.83 (0.73, 0.92) | 0.68 (0.60, 0.91) | 0.77 (0.59, 0.86) | 0.4 | 0.7 |
| Unknown | 0 | 1 | 0 | ||
| aZn | 11.75 (10.80, 13.10) | 11.70 (10.90, 13.30) | 10.60 (9.60, 13.10) | 0.4 | 0.7 |
| Unknown | 0 | 1 | 0 | ||
| aFE | 15 (9, 18) | 13 (12, 19) | 17 (11, 19) | 0.8 | >0.9 |
| Unknown | 0 | 1 | 0 | ||
| aVKFE | 72 (66, 78) | 73 (63, 77) | 67 (62, 74) | 0.2 | 0.4 |
| Unknown | 0 | 1 | 0 | ||
| aFERR | 22 (17, 30) | 19 (15, 26) | 16 (12, 22) | 0.10 | 0.3 |
| Unknown | 0 | 1 | 0 | ||
| aTRF | 2.86 (2.63, 3.09) | 2.88 (2.51, 3.05) | 2.66 (2.47, 2.95) | 0.2 | 0.4 |
| Unknown | 0 | 1 | 0 | ||
| aSATTRF | 20 (15, 25) | 20 (14, 27) | 25 (17, 30) | 0.6 | 0.8 |
| Unknown | 0 | 1 | 0 | ||
| aTRFINDEX | 1.13 (0.95, 1.40) | 1.28 (1.03, 1.39) | 1.20 (1.14, 1.43) | 0.3 | 0.6 |
| Unknown | 0 | 1 | 0 | ||
| aSTRF | 1.49 (1.36, 1.63) | 1.60 (1.40, 1.67) | 1.54 (1.36, 1.66) | 0.6 | 0.8 |
| Unknown | 0 | 1 | 0 | ||
| aHGB | 127 (122, 132) | 129 (123, 135) | 124 (117, 128) | 0.090 | 0.3 |
| Unknown | 0 | 1 | 0 | ||
| aMCV | 80.25 (78.40, 82.20) | 78.70 (76.90, 80.30) | 82.70 (80.10, 84.20) | 0.002 | 0.022 |
| Unknown | 0 | 1 | 0 | ||
| aPTH | 2.55 (1.80, 3.10) | 2.80 (1.90, 3.30) | 2.70 (2.30, 3.50) | 0.8 | 0.9 |
| Unknown | 0 | 1 | 0 | ||
| aCros | 1.24 (0.94, 1.52) | 1.24 (1.12, 1.41) | 1.25 (1.14, 1.41) | >0.9 | >0.9 |
| Unknown | 0 | 1 | 0 | ||
| aP1NP | 454 (397, 511) | 492 (442, 649) | 572 (519, 644) | 0.013 | 0.090 |
| Unknown | 0 | 1 | 0 | ||
| aUI | 173 (140, 256) | 126 (85, 182) | 110 (75, 160) | 0.032 | 0.2 |
| Unknown | 2 | 4 | 3 | ||
| aUREA | 4.50 (4.00, 5.40) | 4.70 (4.30, 5.80) | 4.10 (3.90, 4.80) | 0.083 | 0.3 |
| Unknown | 0 | 1 | 0 | ||
| aCREA | 33 (28, 37) | 31 (27, 36) | 30 (27, 33) | 0.2 | 0.4 |
| Unknown | 0 | 1 | 0 | ||
| aUA | 222 (209, 245) | 236 (221, 249) | 226 (202, 261) | 0.6 | 0.8 |
| Unknown | 0 | 1 | 0 | ||
| aVIT_AKTB12 | 118 (94, 133) | 95 (81, 135) | 143 (102, 228) | 0.070 | 0.3 |
| Unknown | 0 | 1 | 0 | ||
| aHCY | 8.50 (8.00, 10.00) | 7.95 (6.90, 10.00) | 7.65 (6.30, 8.60) | 0.13 | 0.3 |
| Unknown | 0 | 6 | 3 | ||
| aMMA | 204 (169, 239) | 170 (144, 257) | 155 (136, 202) | 0.067 | 0.3 |
| Unknown | 0 | 1 | 0 | ||
| aVIT_D | 70 (59, 87) | 85 (70, 97) | 94 (77, 104) | 0.035 | 0.2 |
| Unknown | 0 | 1 | 0 | ||
| aFOLAT | 11.1 (9.2, 13.8) | 17.5 (15.0, 18.8) | 17.2 (13.1, 21.0) | <0.001 | 0.004 |
| Unknown | 0 | 1 | 0 | ||
| aIGF1 | 156 (107, 192) | 154 (118, 183) | 105 (81, 137) | 0.065 | 0.3 |
| Unknown | 1 | 2 | 1 | ||
| aAL_child | 4 (18%) | 4 (18%) | 2 (9.5%) | 0.8 | 0.9 |
| aSUP_VEG1 | 0 (0%) | 4 (18%) | 2 (9.5%) | 0.11 | 0.3 |
| aSup_B12 | 0 (0%) | 18 (82%) | 16 (76%) | <0.001 | <0.001 |
| aSUP_FOL | 1 (4.5%) | 1 (4.5%) | 1 (4.8%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 0 (0%) | 1 (4.8%) | 0.3 | 0.6 |
| aSUP_vitB1 | 0 (0%) | 2 (9.1%) | 2 (9.5%) | 0.5 | 0.7 |
| aSUP_vit.B5 | 0 (0%) | 2 (9.1%) | 2 (9.5%) | 0.5 | 0.7 |
| aSUP_D | 9 (41%) | 19 (86%) | 15 (71%) | 0.005 | 0.044 |
| aSUP_Mg | 0 (0%) | 4 (18%) | 3 (14%) | 0.11 | 0.3 |
| aSUP_Zn | 0 (0%) | 0 (0%) | 4 (19%) | 0.009 | 0.068 |
| aSUP_Se | 0 (0%) | 0 (0%) | 2 (9.5%) | 0.10 | 0.3 |
| aSUP_Ca | 0 (0%) | 2 (9.1%) | 2 (9.5%) | 0.5 | 0.7 |
| aSUP_Fe | 1 (4.5%) | 3 (14%) | 2 (9.5%) | 0.7 | 0.9 |
| aSUP_Iod | 0 (0%) | 3 (14%) | 4 (19%) | 0.087 | 0.3 |
| aSUP_Ѡ3 | 3 (14%) | 11 (50%) | 16 (76%) | <0.001 | 0.004 |
| aSUP_CHLO | 0 (0%) | 3 (14%) | 0 (0%) | 0.10 | 0.3 |
| aSUP_ALG | |||||
| 0 | 22 (100%) | 22 (100%) | 21 (100%) | ||
| aSUP_GB | 0 (0%) | 1 (4.5%) | 0 (0%) | >0.9 | >0.9 |
| aSUP_FORT | 0 (0%) | 1 (4.5%) | 0 (0%) | >0.9 | >0.9 |
| aSUP_PROB | 1 (4.5%) | 4 (18%) | 0 (0%) | 0.12 | 0.3 |
| aSUP_OTH | 9 (41%) | 5 (23%) | 2 (9.5%) | 0.056 | 0.3 |
| aUr_Krea | 5.3 (4.8, 8.5) | 5.1 (3.4, 6.9) | 4.1 (1.6, 9.0) | 0.5 | 0.7 |
| aUr_Ca | 1.41 (0.51, 2.39) | 1.76 (0.37, 3.47) | 0.61 (0.28, 1.26) | 0.2 | 0.4 |
| aCa_per_Krea | 0.26 (0.12, 0.46) | 0.33 (0.11, 0.78) | 0.21 (0.08, 0.38) | 0.3 | 0.6 |
| aI_per_Krea | 259 (189, 440) | 169 (136, 366) | 339 (107, 404) | 0.6 | 0.8 |
| Unknown | 2 | 4 | 3 | ||
| aP_per_Krea | 3.31 (2.59, 5.41) | 3.36 (1.56, 4.83) | 1.66 (1.42, 3.00) | <0.001 | 0.011 |
| aBiW | 3,290 (3,018, 3,600) | 3,325 (2,990, 3,680) | 3,425 (2,785, 3,720) | >0.9 | >0.9 |
| Unknown | 0 | 0 | 1 | ||
| aBREAKS | 1 (4.5%) | 0 (0%) | 3 (14%) | 0.12 | 0.3 |
| 1
Median (Q1, Q3); n (%) |
|||||
| 2
Kruskal-Wallis rank sum test; Pearson’s Chi-squared test; Fisher’s exact test |
|||||
| 3
False discovery rate correction for multiple testing |
|||||
Open code
DatChar_child_old_df <- DatChar_child_old$table_body %>%
as_tibble()2.2.2.2 OM vs VG
Open code
DatChar_child_old_OM_VG <- run(
dat_child_old_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'OM' | GRP == 'VG') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("OM vs VG, only children >3 year old included") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_old_OM_VG', reuse=TRUE)
DatChar_child_old_OM_VGCharacteristic |
OM |
VG |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 5.51 (4.27, 6.30) | 5.28 (4.40, 6.89) | 0.8 | >0.9 |
| SEX | 0.2 | 0.8 | ||
| F | 13 (59%) | 9 (41%) | ||
| M | 9 (41%) | 13 (59%) | ||
| aBreastFeed_full | 6.00 (5.00, 6.00) | 7.00 (6.00, 8.00) | <0.001 | 0.002 |
| aBreastFeed_total | 10 (8, 16) | 18 (15, 22) | 0.002 | 0.030 |
| Unknown | 3 | 0 | ||
| aBreastFeed_full_stopped | ||||
| 1 | 22 (100%) | 22 (100%) | ||
| aBreastFeed_total_stopped | ||||
| 1 | 19 (100%) | 22 (100%) | ||
| Unknown | 3 | 0 | ||
| dev_delay | 1 (4.5%) | 1 (4.5%) | >0.9 | >0.9 |
| aMASS_Perc | 52 (28, 76) | 62 (27, 65) | 0.9 | >0.9 |
| aHEIGHT_Perc | 41 (18, 76) | 57 (37, 74) | 0.6 | >0.9 |
| aBMI_PERC | 46 (34, 63) | 46 (31, 58) | 0.7 | >0.9 |
| aM_per_H_PERC | 47 (29, 63) | 47 (32, 58) | 0.5 | >0.9 |
| aGLY | 4.28 (3.97, 4.74) | 4.26 (3.79, 4.72) | 0.8 | >0.9 |
| Unknown | 0 | 1 | ||
| aTC | 4.05 (3.60, 4.26) | 3.70 (3.19, 4.32) | 0.3 | 0.8 |
| Unknown | 0 | 1 | ||
| aHDL | 1.35 (1.03, 1.68) | 1.31 (1.10, 1.43) | 0.5 | >0.9 |
| Unknown | 0 | 1 | ||
| aLDL | 2.15 (1.83, 2.26) | 2.11 (1.79, 2.49) | >0.9 | >0.9 |
| Unknown | 0 | 1 | ||
| aTG | 0.89 (0.70, 1.22) | 0.62 (0.56, 0.92) | 0.093 | 0.6 |
| Unknown | 0 | 1 | ||
| aCa | 2.50 (2.44, 2.55) | 2.50 (2.45, 2.58) | 0.8 | >0.9 |
| Unknown | 0 | 1 | ||
| aP | 1.65 (1.48, 1.77) | 1.54 (1.44, 1.63) | 0.3 | 0.8 |
| Unknown | 0 | 1 | ||
| aMg | 0.82 (0.79, 0.85) | 0.83 (0.80, 0.87) | 0.3 | 0.8 |
| Unknown | 0 | 1 | ||
| aSe | 0.83 (0.73, 0.92) | 0.68 (0.60, 0.91) | 0.2 | 0.8 |
| Unknown | 0 | 1 | ||
| aZn | 11.75 (10.80, 13.10) | 11.70 (10.90, 13.30) | >0.9 | >0.9 |
| Unknown | 0 | 1 | ||
| aFE | 15 (9, 18) | 13 (12, 19) | 0.6 | >0.9 |
| Unknown | 0 | 1 | ||
| aVKFE | 72 (66, 78) | 73 (63, 77) | 0.7 | >0.9 |
| Unknown | 0 | 1 | ||
| aFERR | 22 (17, 30) | 19 (15, 26) | 0.7 | >0.9 |
| Unknown | 0 | 1 | ||
| aTRF | 2.86 (2.63, 3.09) | 2.88 (2.51, 3.05) | 0.6 | >0.9 |
| Unknown | 0 | 1 | ||
| aSATTRF | 20 (15, 25) | 20 (14, 27) | >0.9 | >0.9 |
| Unknown | 0 | 1 | ||
| aTRFINDEX | 1.13 (0.95, 1.40) | 1.28 (1.03, 1.39) | 0.5 | >0.9 |
| Unknown | 0 | 1 | ||
| aSTRF | 1.49 (1.36, 1.63) | 1.60 (1.40, 1.67) | 0.3 | 0.8 |
| Unknown | 0 | 1 | ||
| aHGB | 127 (122, 132) | 129 (123, 135) | 0.4 | 0.8 |
| Unknown | 0 | 1 | ||
| aMCV | 80.25 (78.40, 82.20) | 78.70 (76.90, 80.30) | 0.13 | 0.6 |
| Unknown | 0 | 1 | ||
| aPTH | 2.55 (1.80, 3.10) | 2.80 (1.90, 3.30) | >0.9 | >0.9 |
| Unknown | 0 | 1 | ||
| aCros | 1.24 (0.94, 1.52) | 1.24 (1.12, 1.41) | 0.7 | >0.9 |
| Unknown | 0 | 1 | ||
| aP1NP | 454 (397, 511) | 492 (442, 649) | 0.11 | 0.6 |
| Unknown | 0 | 1 | ||
| aUI | 173 (140, 256) | 126 (85, 182) | 0.041 | 0.4 |
| Unknown | 2 | 4 | ||
| aUREA | 4.50 (4.00, 5.40) | 4.70 (4.30, 5.80) | 0.7 | >0.9 |
| Unknown | 0 | 1 | ||
| aCREA | 33 (28, 37) | 31 (27, 36) | 0.7 | >0.9 |
| Unknown | 0 | 1 | ||
| aUA | 222 (209, 245) | 236 (221, 249) | 0.3 | 0.8 |
| Unknown | 0 | 1 | ||
| aVIT_AKTB12 | 118 (94, 133) | 95 (81, 135) | 0.8 | >0.9 |
| Unknown | 0 | 1 | ||
| aHCY | 8.50 (8.00, 10.00) | 7.95 (6.90, 10.00) | 0.3 | 0.8 |
| Unknown | 0 | 6 | ||
| aMMA | 204 (169, 239) | 170 (144, 257) | 0.4 | >0.9 |
| Unknown | 0 | 1 | ||
| aVIT_D | 70 (59, 87) | 85 (70, 97) | 0.047 | 0.4 |
| Unknown | 0 | 1 | ||
| aFOLAT | 11.1 (9.2, 13.8) | 17.5 (15.0, 18.8) | <0.001 | 0.001 |
| Unknown | 0 | 1 | ||
| aIGF1 | 156 (107, 192) | 154 (118, 183) | >0.9 | >0.9 |
| Unknown | 1 | 2 | ||
| aAL_child | 4 (18%) | 4 (18%) | >0.9 | >0.9 |
| aSUP_VEG1 | 0 (0%) | 4 (18%) | 0.11 | 0.6 |
| aSup_B12 | 0 (0%) | 18 (82%) | <0.001 | <0.001 |
| aSUP_FOL | 1 (4.5%) | 1 (4.5%) | >0.9 | >0.9 |
| aSUP_vitA | ||||
| 0 | 22 (100%) | 22 (100%) | ||
| aSUP_vitB1 | 0 (0%) | 2 (9.1%) | 0.5 | >0.9 |
| aSUP_vit.B5 | 0 (0%) | 2 (9.1%) | 0.5 | >0.9 |
| aSUP_D | 9 (41%) | 19 (86%) | 0.002 | 0.028 |
| aSUP_Mg | 0 (0%) | 4 (18%) | 0.11 | 0.6 |
| aSUP_Zn | ||||
| 0 | 22 (100%) | 22 (100%) | ||
| aSUP_Se | ||||
| 0 | 22 (100%) | 22 (100%) | ||
| aSUP_Ca | 0 (0%) | 2 (9.1%) | 0.5 | >0.9 |
| aSUP_Fe | 1 (4.5%) | 3 (14%) | 0.6 | >0.9 |
| aSUP_Iod | 0 (0%) | 3 (14%) | 0.2 | 0.8 |
| aSUP_Ѡ3 | 3 (14%) | 11 (50%) | 0.010 | 0.10 |
| aSUP_CHLO | 0 (0%) | 3 (14%) | 0.2 | 0.8 |
| aSUP_ALG | ||||
| 0 | 22 (100%) | 22 (100%) | ||
| aSUP_GB | 0 (0%) | 1 (4.5%) | >0.9 | >0.9 |
| aSUP_FORT | 0 (0%) | 1 (4.5%) | >0.9 | >0.9 |
| aSUP_PROB | 1 (4.5%) | 4 (18%) | 0.3 | 0.8 |
| aSUP_OTH | 9 (41%) | 5 (23%) | 0.2 | 0.8 |
| aUr_Krea | 5.3 (4.8, 8.5) | 5.1 (3.4, 6.9) | 0.6 | >0.9 |
| aUr_Ca | 1.41 (0.51, 2.39) | 1.76 (0.37, 3.47) | >0.9 | >0.9 |
| aCa_per_Krea | 0.26 (0.12, 0.46) | 0.33 (0.11, 0.78) | 0.5 | >0.9 |
| aI_per_Krea | 259 (189, 440) | 169 (136, 366) | 0.3 | 0.8 |
| Unknown | 2 | 4 | ||
| aP_per_Krea | 3.31 (2.59, 5.41) | 3.36 (1.56, 4.83) | 0.2 | 0.8 |
| aBiW | 3,290 (3,018, 3,600) | 3,325 (2,990, 3,680) | >0.9 | >0.9 |
| aBREAKS | 1 (4.5%) | 0 (0%) | >0.9 | >0.9 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test; Wilcoxon rank sum exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.2.3 OM vs VN
Open code
DatChar_child_old_OM_VN <- run(
dat_child_old_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'OM' | GRP == 'VN') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("OM vs VN, only children >3 year old included") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_old_OM_VN', reuse=TRUE)
DatChar_child_old_OM_VNCharacteristic |
OM |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 5.51 (4.27, 6.30) | 4.67 (3.57, 5.78) | 0.14 | 0.3 |
| SEX | 0.5 | 0.7 | ||
| F | 13 (59%) | 10 (48%) | ||
| M | 9 (41%) | 11 (52%) | ||
| aBreastFeed_full | 6.00 (5.00, 6.00) | 6.00 (6.00, 6.00) | 0.089 | 0.2 |
| aBreastFeed_total | 10 (8, 16) | 18 (12, 35) | 0.004 | 0.049 |
| Unknown | 3 | 2 | ||
| aBreastFeed_full_stopped | ||||
| 1 | 22 (100%) | 21 (100%) | ||
| aBreastFeed_total_stopped | 19 (100%) | 18 (95%) | >0.9 | >0.9 |
| Unknown | 3 | 2 | ||
| dev_delay | 1 (4.5%) | 1 (4.8%) | >0.9 | >0.9 |
| aMASS_Perc | 52 (28, 76) | 40 (27, 67) | 0.4 | 0.6 |
| aHEIGHT_Perc | 41 (18, 76) | 42 (11, 61) | 0.6 | 0.8 |
| aBMI_PERC | 46 (34, 63) | 43 (21, 68) | 0.7 | 0.8 |
| aM_per_H_PERC | 47 (29, 63) | 43 (17, 70) | 0.8 | 0.9 |
| aGLY | 4.28 (3.97, 4.74) | 4.33 (4.19, 4.56) | 0.7 | 0.8 |
| aTC | 4.05 (3.60, 4.26) | 3.42 (3.20, 3.87) | 0.009 | 0.085 |
| aHDL | 1.35 (1.03, 1.68) | 1.23 (1.12, 1.49) | 0.5 | 0.7 |
| aLDL | 2.15 (1.83, 2.26) | 1.71 (1.56, 2.03) | 0.017 | 0.12 |
| aTG | 0.89 (0.70, 1.22) | 0.93 (0.65, 1.10) | 0.8 | 0.9 |
| aCa | 2.50 (2.44, 2.55) | 2.49 (2.47, 2.52) | >0.9 | >0.9 |
| aP | 1.65 (1.48, 1.77) | 1.58 (1.43, 1.67) | 0.3 | 0.5 |
| aMg | 0.82 (0.79, 0.85) | 0.86 (0.81, 0.89) | 0.030 | 0.2 |
| aSe | 0.83 (0.73, 0.92) | 0.77 (0.59, 0.86) | 0.3 | 0.5 |
| aZn | 11.75 (10.80, 13.10) | 10.60 (9.60, 13.10) | 0.4 | 0.6 |
| aFE | 15 (9, 18) | 17 (11, 19) | 0.7 | 0.8 |
| aVKFE | 72 (66, 78) | 67 (62, 74) | 0.10 | 0.2 |
| aFERR | 22 (17, 30) | 16 (12, 22) | 0.058 | 0.2 |
| aTRF | 2.86 (2.63, 3.09) | 2.66 (2.47, 2.95) | 0.087 | 0.2 |
| aSATTRF | 20 (15, 25) | 25 (17, 30) | 0.3 | 0.5 |
| aTRFINDEX | 1.13 (0.95, 1.40) | 1.20 (1.14, 1.43) | 0.14 | 0.3 |
| aSTRF | 1.49 (1.36, 1.63) | 1.54 (1.36, 1.66) | 0.7 | 0.8 |
| aHGB | 127 (122, 132) | 124 (117, 128) | 0.2 | 0.4 |
| aMCV | 80.25 (78.40, 82.20) | 82.70 (80.10, 84.20) | 0.032 | 0.2 |
| aPTH | 2.55 (1.80, 3.10) | 2.70 (2.30, 3.50) | 0.5 | 0.7 |
| aCros | 1.24 (0.94, 1.52) | 1.25 (1.14, 1.41) | 0.7 | 0.8 |
| aP1NP | 454 (397, 511) | 572 (519, 644) | 0.003 | 0.040 |
| aUI | 173 (140, 256) | 110 (75, 160) | 0.019 | 0.12 |
| Unknown | 2 | 3 | ||
| aUREA | 4.50 (4.00, 5.40) | 4.10 (3.90, 4.80) | 0.071 | 0.2 |
| aCREA | 33 (28, 37) | 30 (27, 33) | 0.10 | 0.2 |
| aUA | 222 (209, 245) | 226 (202, 261) | >0.9 | >0.9 |
| aVIT_AKTB12 | 118 (94, 133) | 143 (102, 228) | 0.060 | 0.2 |
| aHCY | 8.50 (8.00, 10.00) | 7.65 (6.30, 8.60) | 0.043 | 0.2 |
| Unknown | 0 | 3 | ||
| aMMA | 204 (169, 239) | 155 (136, 202) | 0.013 | 0.11 |
| aVIT_D | 70 (59, 87) | 94 (77, 104) | 0.022 | 0.12 |
| aFOLAT | 11.1 (9.2, 13.8) | 17.2 (13.1, 21.0) | <0.001 | 0.016 |
| aIGF1 | 156 (107, 192) | 105 (81, 137) | 0.051 | 0.2 |
| Unknown | 1 | 1 | ||
| aAL_child | 4 (18%) | 2 (9.5%) | 0.7 | 0.8 |
| aSUP_VEG1 | 0 (0%) | 2 (9.5%) | 0.2 | 0.4 |
| aSup_B12 | 0 (0%) | 16 (76%) | <0.001 | <0.001 |
| aSUP_FOL | 1 (4.5%) | 1 (4.8%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 1 (4.8%) | 0.5 | 0.7 |
| aSUP_vitB1 | 0 (0%) | 2 (9.5%) | 0.2 | 0.4 |
| aSUP_vit.B5 | 0 (0%) | 2 (9.5%) | 0.2 | 0.4 |
| aSUP_D | 9 (41%) | 15 (71%) | 0.044 | 0.2 |
| aSUP_Mg | 0 (0%) | 3 (14%) | 0.11 | 0.3 |
| aSUP_Zn | 0 (0%) | 4 (19%) | 0.048 | 0.2 |
| aSUP_Se | 0 (0%) | 2 (9.5%) | 0.2 | 0.4 |
| aSUP_Ca | 0 (0%) | 2 (9.5%) | 0.2 | 0.4 |
| aSUP_Fe | 1 (4.5%) | 2 (9.5%) | 0.6 | 0.8 |
| aSUP_Iod | 0 (0%) | 4 (19%) | 0.048 | 0.2 |
| aSUP_Ѡ3 | 3 (14%) | 16 (76%) | <0.001 | 0.001 |
| aSUP_CHLO | ||||
| 0 | 22 (100%) | 21 (100%) | ||
| aSUP_ALG | ||||
| 0 | 22 (100%) | 21 (100%) | ||
| aSUP_GB | ||||
| 0 | 22 (100%) | 21 (100%) | ||
| aSUP_FORT | ||||
| 0 | 22 (100%) | 21 (100%) | ||
| aSUP_PROB | 1 (4.5%) | 0 (0%) | >0.9 | >0.9 |
| aSUP_OTH | 9 (41%) | 2 (9.5%) | 0.018 | 0.12 |
| aUr_Krea | 5.3 (4.8, 8.5) | 4.1 (1.6, 9.0) | 0.2 | 0.4 |
| aUr_Ca | 1.41 (0.51, 2.39) | 0.61 (0.28, 1.26) | 0.11 | 0.3 |
| aCa_per_Krea | 0.26 (0.12, 0.46) | 0.21 (0.08, 0.38) | 0.3 | 0.4 |
| aI_per_Krea | 259 (189, 440) | 339 (107, 404) | 0.6 | 0.8 |
| Unknown | 2 | 3 | ||
| aP_per_Krea | 3.31 (2.59, 5.41) | 1.66 (1.42, 3.00) | <0.001 | 0.002 |
| aBiW | 3,290 (3,018, 3,600) | 3,425 (2,785, 3,720) | >0.9 | >0.9 |
| Unknown | 0 | 1 | ||
| aBREAKS | 1 (4.5%) | 3 (14%) | 0.3 | 0.5 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test; Wilcoxon rank sum exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.2.4 VG vs VN
Open code
DatChar_child_old_VG_VN <- run(
dat_child_old_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'VG' | GRP == 'VN') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("VG vs VN, only children >3 year old included") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_old_VG_VN', reuse=TRUE)
DatChar_child_old_VG_VNCharacteristic |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 5.28 (4.40, 6.89) | 4.67 (3.57, 5.78) | 0.063 | 0.4 |
| SEX | 0.7 | >0.9 | ||
| F | 9 (41%) | 10 (48%) | ||
| M | 13 (59%) | 11 (52%) | ||
| aBreastFeed_full | 7.00 (6.00, 8.00) | 6.00 (6.00, 6.00) | 0.064 | 0.4 |
| aBreastFeed_total | 18 (15, 22) | 18 (12, 35) | 0.8 | >0.9 |
| Unknown | 0 | 2 | ||
| aBreastFeed_full_stopped | ||||
| 1 | 22 (100%) | 21 (100%) | ||
| aBreastFeed_total_stopped | 22 (100%) | 18 (95%) | 0.5 | 0.9 |
| Unknown | 0 | 2 | ||
| dev_delay | 1 (4.5%) | 1 (4.8%) | >0.9 | >0.9 |
| aMASS_Perc | 62 (27, 65) | 40 (27, 67) | 0.5 | 0.9 |
| aHEIGHT_Perc | 57 (37, 74) | 42 (11, 61) | 0.2 | 0.6 |
| aBMI_PERC | 46 (31, 58) | 43 (21, 68) | 0.9 | >0.9 |
| aM_per_H_PERC | 47 (32, 58) | 43 (17, 70) | 0.7 | >0.9 |
| aGLY | 4.26 (3.79, 4.72) | 4.33 (4.19, 4.56) | 0.8 | >0.9 |
| Unknown | 1 | 0 | ||
| aTC | 3.70 (3.19, 4.32) | 3.42 (3.20, 3.87) | 0.3 | 0.7 |
| Unknown | 1 | 0 | ||
| aHDL | 1.31 (1.10, 1.43) | 1.23 (1.12, 1.49) | >0.9 | >0.9 |
| Unknown | 1 | 0 | ||
| aLDL | 2.11 (1.79, 2.49) | 1.71 (1.56, 2.03) | 0.029 | 0.4 |
| Unknown | 1 | 0 | ||
| aTG | 0.62 (0.56, 0.92) | 0.93 (0.65, 1.10) | 0.10 | 0.5 |
| Unknown | 1 | 0 | ||
| aCa | 2.50 (2.45, 2.58) | 2.49 (2.47, 2.52) | >0.9 | >0.9 |
| Unknown | 1 | 0 | ||
| aP | 1.54 (1.44, 1.63) | 1.58 (1.43, 1.67) | 0.8 | >0.9 |
| Unknown | 1 | 0 | ||
| aMg | 0.83 (0.80, 0.87) | 0.86 (0.81, 0.89) | 0.3 | 0.7 |
| Unknown | 1 | 0 | ||
| aSe | 0.68 (0.60, 0.91) | 0.77 (0.59, 0.86) | 0.9 | >0.9 |
| Unknown | 1 | 0 | ||
| aZn | 11.70 (10.90, 13.30) | 10.60 (9.60, 13.10) | 0.2 | 0.6 |
| Unknown | 1 | 0 | ||
| aFE | 13 (12, 19) | 17 (11, 19) | 0.5 | >0.9 |
| Unknown | 1 | 0 | ||
| aVKFE | 73 (63, 77) | 67 (62, 74) | 0.2 | 0.7 |
| Unknown | 1 | 0 | ||
| aFERR | 19 (15, 26) | 16 (12, 22) | 0.076 | 0.4 |
| Unknown | 1 | 0 | ||
| aTRF | 2.88 (2.51, 3.05) | 2.66 (2.47, 2.95) | 0.2 | 0.7 |
| Unknown | 1 | 0 | ||
| aSATTRF | 20 (14, 27) | 25 (17, 30) | 0.4 | 0.9 |
| Unknown | 1 | 0 | ||
| aTRFINDEX | 1.28 (1.03, 1.39) | 1.20 (1.14, 1.43) | 0.3 | 0.8 |
| Unknown | 1 | 0 | ||
| aSTRF | 1.60 (1.40, 1.67) | 1.54 (1.36, 1.66) | 0.5 | 0.9 |
| Unknown | 1 | 0 | ||
| aHGB | 129 (123, 135) | 124 (117, 128) | 0.036 | 0.4 |
| Unknown | 1 | 0 | ||
| aMCV | 78.70 (76.90, 80.30) | 82.70 (80.10, 84.20) | <0.001 | 0.043 |
| Unknown | 1 | 0 | ||
| aPTH | 2.80 (1.90, 3.30) | 2.70 (2.30, 3.50) | 0.6 | >0.9 |
| Unknown | 1 | 0 | ||
| aCros | 1.24 (1.12, 1.41) | 1.25 (1.14, 1.41) | >0.9 | >0.9 |
| Unknown | 1 | 0 | ||
| aP1NP | 492 (442, 649) | 572 (519, 644) | 0.2 | 0.6 |
| Unknown | 1 | 0 | ||
| aUI | 126 (85, 182) | 110 (75, 160) | 0.6 | >0.9 |
| Unknown | 4 | 3 | ||
| aUREA | 4.70 (4.30, 5.80) | 4.10 (3.90, 4.80) | 0.045 | 0.4 |
| Unknown | 1 | 0 | ||
| aCREA | 31 (27, 36) | 30 (27, 33) | 0.2 | 0.6 |
| Unknown | 1 | 0 | ||
| aUA | 236 (221, 249) | 226 (202, 261) | 0.5 | 0.9 |
| Unknown | 1 | 0 | ||
| aVIT_AKTB12 | 95 (81, 135) | 143 (102, 228) | 0.038 | 0.4 |
| Unknown | 1 | 0 | ||
| aHCY | 7.95 (6.90, 10.00) | 7.65 (6.30, 8.60) | 0.5 | 0.9 |
| Unknown | 6 | 3 | ||
| aMMA | 170 (144, 257) | 155 (136, 202) | 0.3 | 0.7 |
| Unknown | 1 | 0 | ||
| aVIT_D | 85 (70, 97) | 94 (77, 104) | 0.4 | 0.8 |
| Unknown | 1 | 0 | ||
| aFOLAT | 17.5 (15.0, 18.8) | 17.2 (13.1, 21.0) | 0.8 | >0.9 |
| Unknown | 1 | 0 | ||
| aIGF1 | 154 (118, 183) | 105 (81, 137) | 0.039 | 0.4 |
| Unknown | 2 | 1 | ||
| aAL_child | 4 (18%) | 2 (9.5%) | 0.7 | >0.9 |
| aSUP_VEG1 | 4 (18%) | 2 (9.5%) | 0.7 | >0.9 |
| aSup_B12 | 18 (82%) | 16 (76%) | 0.7 | >0.9 |
| aSUP_FOL | 1 (4.5%) | 1 (4.8%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 1 (4.8%) | 0.5 | 0.9 |
| aSUP_vitB1 | 2 (9.1%) | 2 (9.5%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 2 (9.1%) | 2 (9.5%) | >0.9 | >0.9 |
| aSUP_D | 19 (86%) | 15 (71%) | 0.3 | 0.7 |
| aSUP_Mg | 4 (18%) | 3 (14%) | >0.9 | >0.9 |
| aSUP_Zn | 0 (0%) | 4 (19%) | 0.048 | 0.4 |
| aSUP_Se | 0 (0%) | 2 (9.5%) | 0.2 | 0.7 |
| aSUP_Ca | 2 (9.1%) | 2 (9.5%) | >0.9 | >0.9 |
| aSUP_Fe | 3 (14%) | 2 (9.5%) | >0.9 | >0.9 |
| aSUP_Iod | 3 (14%) | 4 (19%) | 0.7 | >0.9 |
| aSUP_Ѡ3 | 11 (50%) | 16 (76%) | 0.076 | 0.4 |
| aSUP_CHLO | 3 (14%) | 0 (0%) | 0.2 | 0.7 |
| aSUP_ALG | ||||
| 0 | 22 (100%) | 21 (100%) | ||
| aSUP_GB | 1 (4.5%) | 0 (0%) | >0.9 | >0.9 |
| aSUP_FORT | 1 (4.5%) | 0 (0%) | >0.9 | >0.9 |
| aSUP_PROB | 4 (18%) | 0 (0%) | 0.11 | 0.5 |
| aSUP_OTH | 5 (23%) | 2 (9.5%) | 0.4 | 0.9 |
| aUr_Krea | 5.1 (3.4, 6.9) | 4.1 (1.6, 9.0) | 0.4 | 0.9 |
| aUr_Ca | 1.76 (0.37, 3.47) | 0.61 (0.28, 1.26) | 0.12 | 0.5 |
| aCa_per_Krea | 0.33 (0.11, 0.78) | 0.21 (0.08, 0.38) | 0.2 | 0.6 |
| aI_per_Krea | 169 (136, 366) | 339 (107, 404) | >0.9 | >0.9 |
| Unknown | 4 | 3 | ||
| aP_per_Krea | 3.36 (1.56, 4.83) | 1.66 (1.42, 3.00) | 0.024 | 0.4 |
| aBiW | 3,325 (2,990, 3,680) | 3,425 (2,785, 3,720) | >0.9 | >0.9 |
| Unknown | 0 | 1 | ||
| aBREAKS | 0 (0%) | 3 (14%) | 0.11 | 0.5 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test; Wilcoxon rank sum exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.3 Children <3 y.o. characteristics table
2.2.3.1 Overall
Open code
DatChar_child_young <- run(
dat_child_young_tosum %>%
select(-FAM, -ID) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("Supplementary Table 3. Children characteristics according to food preferences, with only children <3 year old included") %>%
add_p() %>%
add_q(),
path = 'gitignore/run/DatChar_child_young', reuse=TRUE)
DatChar_child_youngCharacteristic |
OM |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|---|
| aAGE | 1.50 (1.01, 2.26) | 1.53 (0.72, 2.12) | 1.35 (0.87, 2.12) | 0.9 | >0.9 |
| SEX | 0.8 | >0.9 | |||
| F | 11 (50%) | 9 (60%) | 21 (53%) | ||
| M | 11 (50%) | 6 (40%) | 19 (48%) | ||
| aBreastFeed_full | 6.00 (6.00, 6.00) | 6.00 (5.50, 6.00) | 6.00 (5.00, 6.00) | 0.4 | 0.8 |
| aBreastFeed_total | 10 (9, 14) | 18 (9, 21) | 12 (8, 17) | 0.5 | 0.8 |
| Unknown | 2 | 2 | 4 | ||
| aBreastFeed_full_stopped | 20 (91%) | 11 (73%) | 35 (88%) | 0.3 | 0.8 |
| aBreastFeed_total_stopped | 12 (60%) | 2 (15%) | 15 (42%) | 0.040 | 0.2 |
| Unknown | 2 | 2 | 4 | ||
| dev_delay | |||||
| 0 | 22 (100%) | 15 (100%) | 40 (100%) | ||
| aMASS_Perc | 63 (33, 79) | 48 (30, 74) | 34 (14, 68) | 0.2 | 0.7 |
| aHEIGHT_Perc | 43 (33, 75) | 51 (28, 68) | 38 (14, 64) | 0.3 | 0.8 |
| aBMI_PERC | 55 (45, 79) | 56 (42, 77) | 56 (35, 70) | 0.7 | >0.9 |
| aM_per_H_PERC | 58 (45, 79) | 61 (39, 70) | 53 (39, 66) | 0.5 | 0.9 |
| aGLY | 4.48 (4.29, 4.62) | 4.66 (4.31, 4.85) | 4.42 (4.21, 4.65) | 0.4 | 0.8 |
| Unknown | 1 | 2 | 6 | ||
| aTC | 3.97 (3.07, 4.40) | 3.89 (3.43, 4.30) | 3.90 (3.43, 4.03) | 0.8 | >0.9 |
| Unknown | 1 | 2 | 6 | ||
| aHDL | 1.10 (0.84, 1.38) | 1.06 (1.00, 1.27) | 1.25 (0.94, 1.36) | 0.7 | >0.9 |
| Unknown | 1 | 2 | 6 | ||
| aLDL | 2.00 (1.50, 2.79) | 2.30 (1.92, 2.62) | 1.98 (1.65, 2.24) | 0.2 | 0.7 |
| Unknown | 1 | 2 | 6 | ||
| aTG | 1.14 (0.93, 1.48) | 0.80 (0.67, 1.22) | 1.09 (0.77, 1.47) | 0.4 | 0.8 |
| Unknown | 1 | 2 | 6 | ||
| aCa | 2.65 (2.54, 2.72) | 2.64 (2.60, 2.72) | 2.63 (2.53, 2.68) | 0.8 | >0.9 |
| Unknown | 1 | 2 | 5 | ||
| aP | 1.70 (1.66, 1.80) | 1.79 (1.69, 1.83) | 1.72 (1.62, 1.83) | 0.7 | >0.9 |
| Unknown | 1 | 2 | 5 | ||
| aMg | 0.87 (0.82, 0.90) | 0.89 (0.85, 0.97) | 0.88 (0.84, 0.92) | 0.4 | 0.8 |
| Unknown | 1 | 2 | 5 | ||
| aSe | 0.75 (0.68, 0.95) | 0.73 (0.63, 0.90) | 0.75 (0.53, 0.94) | >0.9 | >0.9 |
| Unknown | 1 | 3 | 6 | ||
| aZn | 11.70 (10.70, 13.40) | 10.80 (10.25, 11.40) | 10.65 (9.80, 11.80) | 0.2 | 0.7 |
| Unknown | 1 | 3 | 6 | ||
| aFE | 9.6 (8.3, 14.6) | 10.2 (5.4, 12.5) | 11.1 (7.6, 17.1) | 0.4 | 0.8 |
| Unknown | 1 | 2 | 5 | ||
| aVKFE | 75 (72, 79) | 73 (69, 75) | 71 (66, 77) | 0.3 | 0.8 |
| Unknown | 1 | 2 | 6 | ||
| aFERR | 15 (9, 21) | 11 (9, 14) | 12 (9, 16) | 0.4 | 0.8 |
| Unknown | 1 | 2 | 5 | ||
| aTRF | 2.97 (2.85, 3.15) | 2.90 (2.73, 2.99) | 2.82 (2.60, 3.04) | 0.3 | 0.8 |
| Unknown | 1 | 2 | 5 | ||
| aSATTRF | 13 (12, 18) | 14 (7, 18) | 16 (11, 25) | 0.4 | 0.8 |
| Unknown | 1 | 2 | 5 | ||
| aTRFINDEX | 1.64 (1.33, 2.06) | 1.58 (1.43, 1.79) | 1.54 (1.32, 1.96) | >0.9 | >0.9 |
| Unknown | 1 | 2 | 5 | ||
| aSTRF | 1.79 (1.71, 1.94) | 1.65 (1.38, 1.88) | 1.72 (1.51, 1.99) | 0.4 | 0.8 |
| Unknown | 1 | 2 | 5 | ||
| aHGB | 116 (112, 123) | 117 (108, 122) | 119 (115, 121) | 0.7 | >0.9 |
| Unknown | 3 | 3 | 7 | ||
| aMCV | 76.8 (70.9, 78.8) | 77.6 (75.1, 80.7) | 79.7 (76.8, 80.8) | 0.021 | 0.2 |
| Unknown | 3 | 3 | 7 | ||
| aPTH | 2.50 (1.40, 3.80) | 2.60 (1.75, 3.30) | 3.20 (2.10, 4.00) | 0.2 | 0.7 |
| Unknown | 1 | 3 | 5 | ||
| aCros | 1.15 (0.99, 1.28) | 1.25 (0.91, 1.46) | 1.22 (1.13, 1.43) | 0.4 | 0.8 |
| Unknown | 1 | 3 | 6 | ||
| aP1NP | 920 (585, 1,201) | 986 (843, 1,201) | 988 (669, 1,201) | 0.8 | >0.9 |
| Unknown | 1 | 3 | 6 | ||
| aUI | 169 (127, 232) | 190 (134, 271) | 98 (65, 198) | 0.036 | 0.2 |
| Unknown | 10 | 2 | 9 | ||
| aUREA | 4.30 (3.30, 5.60) | 3.20 (2.70, 3.90) | 3.60 (2.70, 4.40) | 0.10 | 0.4 |
| Unknown | 1 | 2 | 5 | ||
| aCREA | 21 (19, 23) | 20 (19, 23) | 19 (18, 23) | 0.4 | 0.8 |
| Unknown | 1 | 2 | 5 | ||
| aUA | 222 (191, 267) | 223 (175, 241) | 218 (184, 255) | 0.8 | >0.9 |
| Unknown | 1 | 2 | 5 | ||
| aVIT_AKTB12 | 84 (72, 93) | 59 (44, 90) | 138 (89, 187) | <0.001 | 0.005 |
| Unknown | 1 | 3 | 6 | ||
| aHCY | 9.3 (7.4, 12.0) | 9.0 (6.9, 12.6) | 7.1 (6.0, 8.9) | 0.004 | 0.050 |
| Unknown | 1 | 5 | 8 | ||
| aMMA | 280 (248, 386) | 305 (188, 638) | 152 (124, 190) | <0.001 | <0.001 |
| Unknown | 5 | 3 | 10 | ||
| aVIT_D | 82 (67, 98) | 98 (81, 129) | 104 (81, 119) | 0.030 | 0.2 |
| Unknown | 1 | 2 | 5 | ||
| aFOLAT | 14.4 (12.7, 17.2) | 18.2 (16.9, 21.1) | 18.1 (15.6, 22.6) | 0.014 | 0.14 |
| Unknown | 1 | 2 | 6 | ||
| aIGF1 | 70 (48, 107) | 63 (50, 84) | 64 (45, 89) | >0.9 | >0.9 |
| Unknown | 1 | 4 | 11 | ||
| aAL_child | 5 (23%) | 1 (6.7%) | 1 (2.5%) | 0.025 | 0.2 |
| aSUP_VEG1 | 0 (0%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSup_B12 | 0 (0%) | 7 (47%) | 30 (75%) | <0.001 | <0.001 |
| aSUP_FOL | 1 (4.5%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vitB1 | 0 (0%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 0 (0%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_D | 12 (55%) | 14 (93%) | 33 (83%) | 0.015 | 0.14 |
| aSUP_Mg | |||||
| 0 | 22 (100%) | 15 (100%) | 40 (100%) | ||
| aSUP_Zn | 0 (0%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Se | 0 (0%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Ca | 0 (0%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Fe | 1 (4.5%) | 1 (6.7%) | 2 (5.0%) | >0.9 | >0.9 |
| aSUP_Iod | 0 (0%) | 0 (0%) | 2 (5.0%) | 0.7 | >0.9 |
| aSUP_Ѡ3 | 2 (9.1%) | 2 (13%) | 23 (58%) | <0.001 | 0.002 |
| aSUP_CHLO | |||||
| 0 | 22 (100%) | 15 (100%) | 40 (100%) | ||
| aSUP_ALG | |||||
| 0 | 22 (100%) | 15 (100%) | 40 (100%) | ||
| aSUP_GB | |||||
| 0 | 22 (100%) | 15 (100%) | 40 (100%) | ||
| aSUP_FORT | |||||
| 0 | 22 (100%) | 15 (100%) | 40 (100%) | ||
| aSUP_PROB | 2 (9.1%) | 2 (13%) | 0 (0%) | 0.062 | 0.3 |
| aSUP_OTH | 5 (23%) | 4 (27%) | 5 (13%) | 0.4 | 0.8 |
| aUr_Krea | 3.20 (2.00, 4.90) | 2.75 (1.40, 3.80) | 1.80 (1.05, 4.35) | 0.5 | 0.8 |
| Unknown | 9 | 1 | 8 | ||
| aUr_Ca | 0.63 (0.49, 1.94) | 1.07 (0.58, 2.61) | 1.02 (0.26, 2.06) | 0.7 | >0.9 |
| Unknown | 9 | 1 | 8 | ||
| aCa_per_Krea | 0.12 (0.11, 0.78) | 0.49 (0.13, 0.88) | 0.41 (0.22, 0.78) | 0.5 | 0.8 |
| Unknown | 9 | 1 | 8 | ||
| aI_per_Krea | 614 (338, 788) | 563 (325, 1,089) | 402 (263, 786) | 0.4 | 0.8 |
| Unknown | 10 | 2 | 10 | ||
| aP_per_Krea | 6.41 (3.10, 7.35) | 3.53 (2.17, 4.16) | 3.12 (1.66, 4.61) | 0.022 | 0.2 |
| Unknown | 9 | 1 | 8 | ||
| aBiW | 3,430 (3,080, 3,750) | 3,400 (3,200, 3,600) | 3,500 (3,050, 3,650) | >0.9 | >0.9 |
| Unknown | 0 | 0 | 1 | ||
| aBREAKS | 0 (0%) | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| 1
Median (Q1, Q3); n (%) |
|||||
| 2
Kruskal-Wallis rank sum test; Pearson’s Chi-squared test; Fisher’s exact test |
|||||
| 3
False discovery rate correction for multiple testing |
|||||
Open code
DatChar_child_young_df <- DatChar_child_young$table_body %>%
as_tibble()2.2.3.2 OM vs VG
Open code
DatChar_child_young_OM_VG <- run(
dat_child_young_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'OM' | GRP == 'VG') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("OM vs VG, with only children <3 year old included") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_young_OM_VG', reuse=TRUE)
DatChar_child_young_OM_VGCharacteristic |
OM |
VG |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 1.50 (1.01, 2.26) | 1.53 (0.72, 2.12) | 0.8 | >0.9 |
| SEX | 0.5 | >0.9 | ||
| F | 11 (50%) | 9 (60%) | ||
| M | 11 (50%) | 6 (40%) | ||
| aBreastFeed_full | 6.00 (6.00, 6.00) | 6.00 (5.50, 6.00) | >0.9 | >0.9 |
| aBreastFeed_total | 10 (9, 14) | 18 (9, 21) | 0.3 | 0.9 |
| Unknown | 2 | 2 | ||
| aBreastFeed_full_stopped | 20 (91%) | 11 (73%) | 0.2 | 0.9 |
| aBreastFeed_total_stopped | 12 (60%) | 2 (15%) | 0.011 | 0.2 |
| Unknown | 2 | 2 | ||
| dev_delay | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aMASS_Perc | 63 (33, 79) | 48 (30, 74) | 0.6 | >0.9 |
| aHEIGHT_Perc | 43 (33, 75) | 51 (28, 68) | 0.9 | >0.9 |
| aBMI_PERC | 55 (45, 79) | 56 (42, 77) | 0.9 | >0.9 |
| aM_per_H_PERC | 58 (45, 79) | 61 (39, 70) | 0.7 | >0.9 |
| aGLY | 4.48 (4.29, 4.62) | 4.66 (4.31, 4.85) | 0.2 | 0.9 |
| Unknown | 1 | 2 | ||
| aTC | 3.97 (3.07, 4.40) | 3.89 (3.43, 4.30) | 0.9 | >0.9 |
| Unknown | 1 | 2 | ||
| aHDL | 1.10 (0.84, 1.38) | 1.06 (1.00, 1.27) | >0.9 | >0.9 |
| Unknown | 1 | 2 | ||
| aLDL | 2.00 (1.50, 2.79) | 2.30 (1.92, 2.62) | 0.4 | >0.9 |
| Unknown | 1 | 2 | ||
| aTG | 1.14 (0.93, 1.48) | 0.80 (0.67, 1.22) | 0.2 | 0.9 |
| Unknown | 1 | 2 | ||
| aCa | 2.65 (2.54, 2.72) | 2.64 (2.60, 2.72) | 0.8 | >0.9 |
| Unknown | 1 | 2 | ||
| aP | 1.70 (1.66, 1.80) | 1.79 (1.69, 1.83) | 0.5 | >0.9 |
| Unknown | 1 | 2 | ||
| aMg | 0.87 (0.82, 0.90) | 0.89 (0.85, 0.97) | 0.3 | 0.9 |
| Unknown | 1 | 2 | ||
| aSe | 0.75 (0.68, 0.95) | 0.73 (0.63, 0.90) | 0.8 | >0.9 |
| Unknown | 1 | 3 | ||
| aZn | 11.70 (10.70, 13.40) | 10.80 (10.25, 11.40) | 0.13 | 0.9 |
| Unknown | 1 | 3 | ||
| aFE | 10 (8, 15) | 10 (5, 13) | 0.7 | >0.9 |
| Unknown | 1 | 2 | ||
| aVKFE | 75 (72, 79) | 73 (69, 75) | 0.3 | 0.9 |
| Unknown | 1 | 2 | ||
| aFERR | 15 (9, 21) | 11 (9, 14) | 0.3 | 0.9 |
| Unknown | 1 | 2 | ||
| aTRF | 2.97 (2.85, 3.15) | 2.90 (2.73, 2.99) | 0.3 | 0.9 |
| Unknown | 1 | 2 | ||
| aSATTRF | 13 (12, 18) | 14 (7, 18) | 0.8 | >0.9 |
| Unknown | 1 | 2 | ||
| aTRFINDEX | 1.64 (1.33, 2.06) | 1.58 (1.43, 1.79) | >0.9 | >0.9 |
| Unknown | 1 | 2 | ||
| aSTRF | 1.79 (1.71, 1.94) | 1.65 (1.38, 1.88) | 0.2 | 0.9 |
| Unknown | 1 | 2 | ||
| aHGB | 116 (112, 123) | 117 (108, 122) | 0.8 | >0.9 |
| Unknown | 3 | 3 | ||
| aMCV | 76.8 (70.9, 78.8) | 77.6 (75.1, 80.7) | 0.2 | 0.9 |
| Unknown | 3 | 3 | ||
| aPTH | 2.50 (1.40, 3.80) | 2.60 (1.75, 3.30) | >0.9 | >0.9 |
| Unknown | 1 | 3 | ||
| aCros | 1.15 (0.99, 1.28) | 1.25 (0.91, 1.46) | 0.7 | >0.9 |
| Unknown | 1 | 3 | ||
| aP1NP | 920 (585, 1,201) | 986 (843, 1,201) | 0.7 | >0.9 |
| Unknown | 1 | 3 | ||
| aUI | 169 (127, 232) | 190 (134, 271) | 0.7 | >0.9 |
| Unknown | 10 | 2 | ||
| aUREA | 4.30 (3.30, 5.60) | 3.20 (2.70, 3.90) | 0.063 | 0.7 |
| Unknown | 1 | 2 | ||
| aCREA | 21 (19, 23) | 20 (19, 23) | 0.5 | >0.9 |
| Unknown | 1 | 2 | ||
| aUA | 222 (191, 267) | 223 (175, 241) | 0.6 | >0.9 |
| Unknown | 1 | 2 | ||
| aVIT_AKTB12 | 84 (72, 93) | 59 (44, 90) | 0.2 | 0.9 |
| Unknown | 1 | 3 | ||
| aHCY | 9.30 (7.40, 12.00) | 9.00 (6.90, 12.60) | 0.9 | >0.9 |
| Unknown | 1 | 5 | ||
| aMMA | 280 (248, 386) | 305 (188, 638) | 0.9 | >0.9 |
| Unknown | 5 | 3 | ||
| aVIT_D | 82 (67, 98) | 98 (81, 129) | 0.11 | 0.9 |
| Unknown | 1 | 2 | ||
| aFOLAT | 14.4 (12.7, 17.2) | 18.2 (16.9, 21.1) | 0.017 | 0.2 |
| Unknown | 1 | 2 | ||
| aIGF1 | 70 (48, 107) | 63 (50, 84) | 0.7 | >0.9 |
| Unknown | 1 | 4 | ||
| aAL_child | 5 (23%) | 1 (6.7%) | 0.4 | >0.9 |
| aSUP_VEG1 | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSup_B12 | 0 (0%) | 7 (47%) | <0.001 | 0.035 |
| aSUP_FOL | 1 (4.5%) | 0 (0%) | >0.9 | >0.9 |
| aSUP_vitA | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_vitB1 | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_vit.B5 | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_D | 12 (55%) | 14 (93%) | 0.014 | 0.2 |
| aSUP_Mg | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_Zn | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_Se | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_Ca | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_Fe | 1 (4.5%) | 1 (6.7%) | >0.9 | >0.9 |
| aSUP_Iod | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_Ѡ3 | 2 (9.1%) | 2 (13%) | >0.9 | >0.9 |
| aSUP_CHLO | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_ALG | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_GB | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_FORT | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| aSUP_PROB | 2 (9.1%) | 2 (13%) | >0.9 | >0.9 |
| aSUP_OTH | 5 (23%) | 4 (27%) | >0.9 | >0.9 |
| aUr_Krea | 3.20 (2.00, 4.90) | 2.75 (1.40, 3.80) | 0.7 | >0.9 |
| Unknown | 9 | 1 | ||
| aUr_Ca | 0.63 (0.49, 1.94) | 1.07 (0.58, 2.61) | 0.5 | >0.9 |
| Unknown | 9 | 1 | ||
| aCa_per_Krea | 0.12 (0.11, 0.78) | 0.49 (0.13, 0.88) | 0.2 | 0.9 |
| Unknown | 9 | 1 | ||
| aI_per_Krea | 614 (338, 788) | 563 (325, 1,089) | >0.9 | >0.9 |
| Unknown | 10 | 2 | ||
| aP_per_Krea | 6.41 (3.10, 7.35) | 3.53 (2.17, 4.16) | 0.076 | 0.7 |
| Unknown | 9 | 1 | ||
| aBiW | 3,430 (3,080, 3,750) | 3,400 (3,200, 3,600) | >0.9 | >0.9 |
| aBREAKS | ||||
| 0 | 22 (100%) | 15 (100%) | ||
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test; Wilcoxon rank sum exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.3.3 OM vs VN
Open code
DatChar_child_young_OM_VN <- run(
dat_child_young_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'OM' | GRP == 'VN') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("OM vs VN, with only children <3 year old included") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_young_OM_VN', reuse=TRUE)
DatChar_child_young_OM_VNCharacteristic |
OM |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 1.50 (1.01, 2.26) | 1.35 (0.87, 2.12) | 0.7 | >0.9 |
| SEX | 0.9 | >0.9 | ||
| F | 11 (50%) | 21 (53%) | ||
| M | 11 (50%) | 19 (48%) | ||
| aBreastFeed_full | 6.00 (6.00, 6.00) | 6.00 (5.00, 6.00) | 0.2 | 0.6 |
| aBreastFeed_total | 10 (9, 14) | 12 (8, 17) | 0.6 | >0.9 |
| Unknown | 2 | 4 | ||
| aBreastFeed_full_stopped | 20 (91%) | 35 (88%) | >0.9 | >0.9 |
| aBreastFeed_total_stopped | 12 (60%) | 15 (42%) | 0.2 | 0.5 |
| Unknown | 2 | 4 | ||
| dev_delay | ||||
| 0 | 22 (100%) | 40 (100%) | ||
| aMASS_Perc | 63 (33, 79) | 34 (14, 68) | 0.11 | 0.5 |
| aHEIGHT_Perc | 43 (33, 75) | 38 (14, 64) | 0.2 | 0.5 |
| aBMI_PERC | 55 (45, 79) | 56 (35, 70) | 0.4 | 0.8 |
| aM_per_H_PERC | 58 (45, 79) | 53 (39, 66) | 0.3 | 0.6 |
| aGLY | 4.48 (4.29, 4.62) | 4.42 (4.21, 4.65) | >0.9 | >0.9 |
| Unknown | 1 | 6 | ||
| aTC | 3.97 (3.07, 4.40) | 3.90 (3.43, 4.03) | 0.5 | 0.9 |
| Unknown | 1 | 6 | ||
| aHDL | 1.10 (0.84, 1.38) | 1.25 (0.94, 1.36) | 0.5 | 0.9 |
| Unknown | 1 | 6 | ||
| aLDL | 2.00 (1.50, 2.79) | 1.98 (1.65, 2.24) | 0.6 | >0.9 |
| Unknown | 1 | 6 | ||
| aTG | 1.14 (0.93, 1.48) | 1.09 (0.77, 1.47) | 0.7 | >0.9 |
| Unknown | 1 | 6 | ||
| aCa | 2.65 (2.54, 2.72) | 2.63 (2.53, 2.68) | 0.7 | >0.9 |
| Unknown | 1 | 5 | ||
| aP | 1.70 (1.66, 1.80) | 1.72 (1.62, 1.83) | 0.8 | >0.9 |
| Unknown | 1 | 5 | ||
| aMg | 0.87 (0.82, 0.90) | 0.88 (0.84, 0.92) | 0.3 | 0.6 |
| Unknown | 1 | 5 | ||
| aSe | 0.75 (0.68, 0.95) | 0.75 (0.53, 0.94) | 0.9 | >0.9 |
| Unknown | 1 | 6 | ||
| aZn | 11.70 (10.70, 13.40) | 10.65 (9.80, 11.80) | 0.083 | 0.4 |
| Unknown | 1 | 6 | ||
| aFE | 9.6 (8.3, 14.6) | 11.1 (7.6, 17.1) | 0.3 | 0.6 |
| Unknown | 1 | 5 | ||
| aVKFE | 75 (72, 79) | 71 (66, 77) | 0.12 | 0.5 |
| Unknown | 1 | 6 | ||
| aFERR | 15 (9, 21) | 12 (9, 16) | 0.3 | 0.6 |
| Unknown | 1 | 5 | ||
| aTRF | 2.97 (2.85, 3.15) | 2.82 (2.60, 3.04) | 0.12 | 0.5 |
| Unknown | 1 | 5 | ||
| aSATTRF | 13 (12, 18) | 16 (11, 25) | 0.3 | 0.6 |
| Unknown | 1 | 5 | ||
| aTRFINDEX | 1.64 (1.33, 2.06) | 1.54 (1.32, 1.96) | 0.9 | >0.9 |
| Unknown | 1 | 5 | ||
| aSTRF | 1.79 (1.71, 1.94) | 1.72 (1.51, 1.99) | 0.4 | 0.7 |
| Unknown | 1 | 5 | ||
| aHGB | 116 (112, 123) | 119 (115, 121) | 0.5 | 0.9 |
| Unknown | 3 | 7 | ||
| aMCV | 76.8 (70.9, 78.8) | 79.7 (76.8, 80.8) | 0.005 | 0.056 |
| Unknown | 3 | 7 | ||
| aPTH | 2.50 (1.40, 3.80) | 3.20 (2.10, 4.00) | 0.2 | 0.5 |
| Unknown | 1 | 5 | ||
| aCros | 1.15 (0.99, 1.28) | 1.22 (1.13, 1.43) | 0.14 | 0.5 |
| Unknown | 1 | 6 | ||
| aP1NP | 920 (585, 1,201) | 988 (669, 1,201) | 0.6 | >0.9 |
| Unknown | 1 | 6 | ||
| aUI | 169 (127, 232) | 98 (65, 198) | 0.025 | 0.14 |
| Unknown | 10 | 9 | ||
| aUREA | 4.30 (3.30, 5.60) | 3.60 (2.70, 4.40) | 0.092 | 0.4 |
| Unknown | 1 | 5 | ||
| aCREA | 21 (19, 23) | 19 (18, 23) | 0.2 | 0.5 |
| Unknown | 1 | 5 | ||
| aUA | 222 (191, 267) | 218 (184, 255) | 0.7 | >0.9 |
| Unknown | 1 | 5 | ||
| aVIT_AKTB12 | 84 (72, 93) | 138 (89, 187) | 0.001 | 0.018 |
| Unknown | 1 | 6 | ||
| aHCY | 9.30 (7.40, 12.00) | 7.10 (6.00, 8.90) | 0.002 | 0.023 |
| Unknown | 1 | 8 | ||
| aMMA | 280 (248, 386) | 152 (124, 190) | <0.001 | <0.001 |
| Unknown | 5 | 10 | ||
| aVIT_D | 82 (67, 98) | 104 (81, 119) | 0.008 | 0.065 |
| Unknown | 1 | 5 | ||
| aFOLAT | 14.4 (12.7, 17.2) | 18.1 (15.6, 22.6) | 0.009 | 0.065 |
| Unknown | 1 | 6 | ||
| aIGF1 | 70 (48, 107) | 64 (45, 89) | 0.8 | >0.9 |
| Unknown | 1 | 11 | ||
| aAL_child | 5 (23%) | 1 (2.5%) | 0.018 | 0.11 |
| aSUP_VEG1 | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSup_B12 | 0 (0%) | 30 (75%) | <0.001 | <0.001 |
| aSUP_FOL | 1 (4.5%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vitB1 | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_D | 12 (55%) | 33 (83%) | 0.018 | 0.11 |
| aSUP_Mg | ||||
| 0 | 22 (100%) | 40 (100%) | ||
| aSUP_Zn | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Se | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Ca | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Fe | 1 (4.5%) | 2 (5.0%) | >0.9 | >0.9 |
| aSUP_Iod | 0 (0%) | 2 (5.0%) | 0.5 | 0.9 |
| aSUP_Ѡ3 | 2 (9.1%) | 23 (58%) | <0.001 | 0.004 |
| aSUP_CHLO | ||||
| 0 | 22 (100%) | 40 (100%) | ||
| aSUP_ALG | ||||
| 0 | 22 (100%) | 40 (100%) | ||
| aSUP_GB | ||||
| 0 | 22 (100%) | 40 (100%) | ||
| aSUP_FORT | ||||
| 0 | 22 (100%) | 40 (100%) | ||
| aSUP_PROB | 2 (9.1%) | 0 (0%) | 0.12 | 0.5 |
| aSUP_OTH | 5 (23%) | 5 (13%) | 0.3 | 0.6 |
| aUr_Krea | 3.20 (2.00, 4.90) | 1.80 (1.05, 4.35) | 0.2 | 0.6 |
| Unknown | 9 | 8 | ||
| aUr_Ca | 0.63 (0.49, 1.94) | 1.02 (0.26, 2.06) | 0.9 | >0.9 |
| Unknown | 9 | 8 | ||
| aCa_per_Krea | 0.12 (0.11, 0.78) | 0.41 (0.22, 0.78) | 0.3 | 0.6 |
| Unknown | 9 | 8 | ||
| aI_per_Krea | 614 (338, 788) | 402 (263, 786) | 0.3 | 0.6 |
| Unknown | 10 | 10 | ||
| aP_per_Krea | 6.41 (3.10, 7.35) | 3.12 (1.66, 4.61) | 0.006 | 0.057 |
| Unknown | 9 | 8 | ||
| aBiW | 3,430 (3,080, 3,750) | 3,500 (3,050, 3,650) | 0.8 | >0.9 |
| Unknown | 0 | 1 | ||
| aBREAKS | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test; Wilcoxon rank sum exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.3.4 VG vs VN
Open code
DatChar_child_young_VG_VN <- run(
dat_child_young_tosum %>%
select(-FAM, -ID) %>%
filter(GRP == 'VG' | GRP == 'VN') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(
by = 'GRP',
type = list(
aBreastFeed_full ~ 'continuous',
aBreastFeed_total ~ 'continuous')) %>%
modify_caption("VG vs VN, with only children <3 year old included") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_child_young_VG_VN', reuse=TRUE)
DatChar_child_young_VG_VNCharacteristic |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 1.53 (0.72, 2.12) | 1.35 (0.87, 2.12) | 0.9 | >0.9 |
| SEX | 0.6 | >0.9 | ||
| F | 9 (60%) | 21 (53%) | ||
| M | 6 (40%) | 19 (48%) | ||
| aBreastFeed_full | 6.00 (5.50, 6.00) | 6.00 (5.00, 6.00) | 0.4 | >0.9 |
| aBreastFeed_total | 18 (9, 21) | 12 (8, 17) | 0.3 | >0.9 |
| Unknown | 2 | 4 | ||
| aBreastFeed_full_stopped | 11 (73%) | 35 (88%) | 0.2 | >0.9 |
| aBreastFeed_total_stopped | 2 (15%) | 15 (42%) | 0.11 | 0.7 |
| Unknown | 2 | 4 | ||
| dev_delay | ||||
| 0 | 15 (100%) | 40 (100%) | ||
| aMASS_Perc | 48 (30, 74) | 34 (14, 68) | 0.3 | >0.9 |
| aHEIGHT_Perc | 51 (28, 68) | 38 (14, 64) | 0.3 | >0.9 |
| aBMI_PERC | 56 (42, 77) | 56 (35, 70) | 0.6 | >0.9 |
| aM_per_H_PERC | 61 (39, 70) | 53 (39, 66) | 0.5 | >0.9 |
| aGLY | 4.66 (4.31, 4.85) | 4.42 (4.21, 4.65) | 0.2 | >0.9 |
| Unknown | 2 | 6 | ||
| aTC | 3.89 (3.43, 4.30) | 3.90 (3.43, 4.03) | 0.7 | >0.9 |
| Unknown | 2 | 6 | ||
| aHDL | 1.06 (1.00, 1.27) | 1.25 (0.94, 1.36) | 0.5 | >0.9 |
| Unknown | 2 | 6 | ||
| aLDL | 2.30 (1.92, 2.62) | 1.98 (1.65, 2.24) | 0.043 | 0.6 |
| Unknown | 2 | 6 | ||
| aTG | 0.80 (0.67, 1.22) | 1.09 (0.77, 1.47) | 0.2 | >0.9 |
| Unknown | 2 | 6 | ||
| aCa | 2.64 (2.60, 2.72) | 2.63 (2.53, 2.68) | 0.5 | >0.9 |
| Unknown | 2 | 5 | ||
| aP | 1.79 (1.69, 1.83) | 1.72 (1.62, 1.83) | 0.4 | >0.9 |
| Unknown | 2 | 5 | ||
| aMg | 0.89 (0.85, 0.97) | 0.88 (0.84, 0.92) | 0.7 | >0.9 |
| Unknown | 2 | 5 | ||
| aSe | 0.73 (0.63, 0.90) | 0.75 (0.53, 0.94) | 0.9 | >0.9 |
| Unknown | 3 | 6 | ||
| aZn | 10.80 (10.25, 11.40) | 10.65 (9.80, 11.80) | >0.9 | >0.9 |
| Unknown | 3 | 6 | ||
| aFE | 10.2 (5.4, 12.5) | 11.1 (7.6, 17.1) | 0.3 | >0.9 |
| Unknown | 2 | 5 | ||
| aVKFE | 73 (69, 75) | 71 (66, 77) | 0.8 | >0.9 |
| Unknown | 2 | 6 | ||
| aFERR | 11 (9, 14) | 12 (9, 16) | 0.6 | >0.9 |
| Unknown | 2 | 5 | ||
| aTRF | 2.90 (2.73, 2.99) | 2.82 (2.60, 3.04) | 0.7 | >0.9 |
| Unknown | 2 | 5 | ||
| aSATTRF | 14 (7, 18) | 16 (11, 25) | 0.3 | >0.9 |
| Unknown | 2 | 5 | ||
| aTRFINDEX | 1.58 (1.43, 1.79) | 1.54 (1.32, 1.96) | >0.9 | >0.9 |
| Unknown | 2 | 5 | ||
| aSTRF | 1.65 (1.38, 1.88) | 1.72 (1.51, 1.99) | 0.4 | >0.9 |
| Unknown | 2 | 5 | ||
| aHGB | 117 (108, 122) | 119 (115, 121) | 0.6 | >0.9 |
| Unknown | 3 | 7 | ||
| aMCV | 77.60 (75.10, 80.70) | 79.70 (76.80, 80.80) | 0.4 | >0.9 |
| Unknown | 3 | 7 | ||
| aPTH | 2.60 (1.75, 3.30) | 3.20 (2.10, 4.00) | 0.11 | 0.7 |
| Unknown | 3 | 5 | ||
| aCros | 1.25 (0.91, 1.46) | 1.22 (1.13, 1.43) | 0.7 | >0.9 |
| Unknown | 3 | 6 | ||
| aP1NP | 986 (843, 1,201) | 988 (669, 1,201) | 0.8 | >0.9 |
| Unknown | 3 | 6 | ||
| aUI | 190 (134, 271) | 98 (65, 198) | 0.060 | 0.6 |
| Unknown | 2 | 9 | ||
| aUREA | 3.20 (2.70, 3.90) | 3.60 (2.70, 4.40) | 0.4 | >0.9 |
| Unknown | 2 | 5 | ||
| aCREA | 20 (19, 23) | 19 (18, 23) | 0.6 | >0.9 |
| Unknown | 2 | 5 | ||
| aUA | 223 (175, 241) | 218 (184, 255) | 0.7 | >0.9 |
| Unknown | 2 | 5 | ||
| aVIT_AKTB12 | 59 (44, 90) | 138 (89, 187) | 0.002 | 0.057 |
| Unknown | 3 | 6 | ||
| aHCY | 9.0 (6.9, 12.6) | 7.1 (6.0, 8.9) | 0.043 | 0.6 |
| Unknown | 5 | 8 | ||
| aMMA | 305 (188, 638) | 152 (124, 190) | <0.001 | 0.015 |
| Unknown | 3 | 10 | ||
| aVIT_D | 98 (81, 129) | 104 (81, 119) | >0.9 | >0.9 |
| Unknown | 2 | 5 | ||
| aFOLAT | 18.2 (16.9, 21.1) | 18.1 (15.6, 22.6) | >0.9 | >0.9 |
| Unknown | 2 | 6 | ||
| aIGF1 | 63 (50, 84) | 64 (45, 89) | >0.9 | >0.9 |
| Unknown | 4 | 11 | ||
| aAL_child | 1 (6.7%) | 1 (2.5%) | 0.5 | >0.9 |
| aSUP_VEG1 | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSup_B12 | 7 (47%) | 30 (75%) | 0.059 | 0.6 |
| aSUP_FOL | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vitA | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vitB1 | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_D | 14 (93%) | 33 (83%) | 0.4 | >0.9 |
| aSUP_Mg | ||||
| 0 | 15 (100%) | 40 (100%) | ||
| aSUP_Zn | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Se | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Ca | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| aSUP_Fe | 1 (6.7%) | 2 (5.0%) | >0.9 | >0.9 |
| aSUP_Iod | 0 (0%) | 2 (5.0%) | >0.9 | >0.9 |
| aSUP_Ѡ3 | 2 (13%) | 23 (58%) | 0.003 | 0.074 |
| aSUP_CHLO | ||||
| 0 | 15 (100%) | 40 (100%) | ||
| aSUP_ALG | ||||
| 0 | 15 (100%) | 40 (100%) | ||
| aSUP_GB | ||||
| 0 | 15 (100%) | 40 (100%) | ||
| aSUP_FORT | ||||
| 0 | 15 (100%) | 40 (100%) | ||
| aSUP_PROB | 2 (13%) | 0 (0%) | 0.071 | 0.6 |
| aSUP_OTH | 4 (27%) | 5 (13%) | 0.2 | >0.9 |
| aUr_Krea | 2.75 (1.40, 3.80) | 1.80 (1.05, 4.35) | 0.5 | >0.9 |
| Unknown | 1 | 8 | ||
| aUr_Ca | 1.07 (0.58, 2.61) | 1.02 (0.26, 2.06) | 0.5 | >0.9 |
| Unknown | 1 | 8 | ||
| aCa_per_Krea | 0.49 (0.13, 0.88) | 0.41 (0.22, 0.78) | 0.8 | >0.9 |
| Unknown | 1 | 8 | ||
| aI_per_Krea | 563 (325, 1,089) | 402 (263, 786) | 0.3 | >0.9 |
| Unknown | 2 | 10 | ||
| aP_per_Krea | 3.53 (2.17, 4.16) | 3.12 (1.66, 4.61) | 0.5 | >0.9 |
| Unknown | 1 | 8 | ||
| aBiW | 3,400 (3,200, 3,600) | 3,500 (3,050, 3,650) | >0.9 | >0.9 |
| Unknown | 0 | 1 | ||
| aBREAKS | 0 (0%) | 1 (2.5%) | >0.9 | >0.9 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum exact test; Pearson’s Chi-squared test; Wilcoxon rank sum test; Fisher’s exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.4 Adults characteristics table
Comparison of clinical outcomes across diet groups in adults
2.2.4.1 Overall
Open code
DatChar_adult <- run(
dat_adult %>%
select(-FAM, -ID) %>%
tbl_summary(by = 'GRP') %>%
modify_caption("Supplementary Table 4. Adults characteristics according to food preferences") %>%
add_p() %>%
add_q(),
path = 'gitignore/run/DatChar_adult', reuse=TRUE)
DatChar_adultCharacteristic |
OM |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|---|
| aAGE | 35.8 (32.8, 40.0) | 36.7 (33.4, 38.2) | 33.9 (31.5, 37.2) | 0.024 | 0.092 |
| SEX | >0.9 | >0.9 | |||
| F | 25 (50%) | 23 (51%) | 47 (51%) | ||
| M | 25 (50%) | 22 (49%) | 45 (49%) | ||
| aBMI | 24.5 (22.4, 26.7) | 22.9 (21.5, 26.1) | 22.6 (20.8, 25.6) | 0.063 | 0.2 |
| aWHR | 0.79 (0.75, 0.85) | 0.78 (0.73, 0.85) | 0.78 (0.73, 0.82) | 0.4 | 0.6 |
| Unknown | 0 | 0 | 4 | ||
| aHEIGHT | 1.76 (1.69, 1.80) | 1.74 (1.72, 1.80) | 1.73 (1.66, 1.81) | 0.6 | 0.7 |
| aMASS | 75 (65, 84) | 72 (65, 80) | 69 (59, 81) | 0.14 | 0.3 |
| aHG | 38 (30, 54) | 43 (32, 51) | 40 (31, 52) | 0.9 | >0.9 |
| Unknown | 1 | 0 | 0 | ||
| aPFAT | 21 (18, 29) | 23 (16, 29) | 21 (15, 26) | 0.4 | 0.5 |
| aFAT | 17 (12, 22) | 17 (11, 23) | 14 (10, 18) | 0.078 | 0.2 |
| aFFM | 54 (48, 68) | 56 (49, 64) | 53 (45, 65) | 0.4 | 0.5 |
| aSBP | 125 (116, 140) | 121 (111, 134) | 121 (112, 134) | 0.2 | 0.4 |
| aDBP | 79 (70, 83) | 79 (73, 86) | 75 (70, 80) | 0.014 | 0.061 |
| aGLY | 4.49 (4.25, 4.77) | 4.44 (4.19, 4.66) | 4.45 (4.13, 4.71) | 0.5 | 0.6 |
| aTC | 4.85 (4.30, 5.40) | 4.28 (3.78, 5.02) | 4.15 (3.65, 4.68) | <0.001 | <0.001 |
| aHDL | 1.53 (1.23, 1.74) | 1.35 (1.20, 1.68) | 1.43 (1.24, 1.69) | 0.6 | 0.8 |
| aLDL | 2.81 (2.44, 3.34) | 2.36 (2.04, 3.10) | 2.23 (1.92, 2.77) | <0.001 | <0.001 |
| aTG | 0.87 (0.57, 1.16) | 0.76 (0.65, 1.02) | 0.74 (0.57, 1.06) | 0.4 | 0.6 |
| aCa | 2.44 (2.38, 2.52) | 2.45 (2.41, 2.50) | 2.46 (2.42, 2.51) | 0.7 | 0.8 |
| aP | 1.12 (1.06, 1.21) | 1.12 (0.97, 1.26) | 1.08 (1.01, 1.21) | 0.5 | 0.6 |
| aMg | 0.79 (0.77, 0.87) | 0.81 (0.78, 0.83) | 0.81 (0.77, 0.85) | >0.9 | >0.9 |
| aSe | 1.00 (0.92, 1.17) | 0.97 (0.67, 1.18) | 0.97 (0.75, 1.18) | 0.4 | 0.5 |
| aZn | 14.05 (12.90, 15.60) | 13.10 (11.70, 14.10) | 12.10 (10.75, 13.80) | <0.001 | <0.001 |
| aFE | 20 (16, 24) | 15 (12, 25) | 19 (15, 25) | 0.2 | 0.3 |
| aVKFE | 68 (62, 74) | 70 (62, 77) | 68 (65, 76) | 0.6 | 0.7 |
| aFERR | 38 (23, 83) | 25 (16, 50) | 26 (14, 35) | 0.003 | 0.015 |
| aTRF | 2.71 (2.46, 2.94) | 2.77 (2.46, 3.07) | 2.70 (2.56, 3.02) | 0.6 | 0.8 |
| aSATTRF | 28 (24, 36) | 22 (17, 39) | 29 (21, 36) | 0.2 | 0.3 |
| aTRFINDEX | 0.73 (0.61, 0.93) | 0.92 (0.64, 1.17) | 0.84 (0.70, 1.02) | 0.015 | 0.061 |
| Unknown | 0 | 1 | 1 | ||
| aSTRF | 1.18 (1.05, 1.32) | 1.25 (1.05, 1.47) | 1.21 (1.01, 1.34) | 0.2 | 0.4 |
| Unknown | 0 | 1 | 0 | ||
| aHGB | 147 (136, 154) | 144 (134, 154) | 145 (135, 156) | 0.8 | 0.8 |
| aMCV | 87.6 (86.0, 89.8) | 86.7 (85.1, 89.5) | 89.7 (87.0, 91.8) | <0.001 | 0.004 |
| aPTH | 2.95 (2.40, 4.00) | 3.00 (2.20, 3.40) | 3.30 (2.70, 4.10) | 0.026 | 0.10 |
| aCros | 0.36 (0.25, 0.56) | 0.36 (0.27, 0.48) | 0.41 (0.30, 0.59) | 0.2 | 0.4 |
| aP1NP | 45 (33, 60) | 43 (37, 61) | 52 (40, 73) | 0.062 | 0.2 |
| aUI | 120 (81, 213) | 94 (41, 171) | 91 (45, 152) | 0.087 | 0.2 |
| Unknown | 8 | 5 | 5 | ||
| aUREA | 4.80 (4.00, 5.70) | 4.40 (3.80, 5.10) | 3.95 (3.20, 4.50) | <0.001 | <0.001 |
| aCREA | 70 (59, 81) | 66 (58, 78) | 64 (56, 72) | 0.036 | 0.12 |
| aUA | 306 (249, 365) | 290 (246, 350) | 300 (247, 348) | >0.9 | >0.9 |
| aVIT_AKTB12 | 84 (71, 109) | 75 (54, 106) | 90 (66, 124) | 0.10 | 0.2 |
| aHCY | 15.2 (11.9, 18.1) | 15.8 (12.7, 21.5) | 14.2 (12.5, 17.1) | 0.2 | 0.4 |
| Unknown | 0 | 10 | 14 | ||
| aMMA | 194 (158, 234) | 236 (161, 305) | 170 (134, 215) | <0.001 | 0.005 |
| aVIT_D | 67 (51, 79) | 73 (59, 88) | 76 (65, 92) | 0.001 | 0.009 |
| aFOLAT | 9.2 (7.3, 11.6) | 12.9 (10.1, 15.4) | 12.6 (9.7, 16.2) | <0.001 | <0.001 |
| aAL_adult | 17 (34%) | 12 (27%) | 12 (13%) | 0.011 | 0.053 |
| aSUP_VEG1 | 0 (0%) | 6 (13%) | 4 (4.3%) | 0.013 | 0.059 |
| aSup_B12 | 1 (2.0%) | 23 (51%) | 76 (83%) | <0.001 | <0.001 |
| aSUP_FOL | 1 (2.0%) | 0 (0%) | 6 (6.5%) | 0.2 | 0.4 |
| aSUP_vitA | 0 (0%) | 0 (0%) | 2 (2.2%) | 0.7 | 0.8 |
| aSUP_vitB1 | 1 (2.0%) | 1 (2.2%) | 2 (2.2%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 1 (2.0%) | 1 (2.2%) | 2 (2.2%) | >0.9 | >0.9 |
| aSUP_D | 17 (34%) | 34 (76%) | 65 (71%) | <0.001 | <0.001 |
| aSUP_Mg | 13 (26%) | 11 (24%) | 12 (13%) | 0.10 | 0.2 |
| aSUP_Zn | 6 (12%) | 6 (13%) | 5 (5.4%) | 0.2 | 0.4 |
| aSUP_Se | 0 (0%) | 1 (2.2%) | 3 (3.3%) | 0.7 | 0.8 |
| aSUP_Ca | 0 (0%) | 3 (6.7%) | 10 (11%) | 0.030 | 0.11 |
| aSUP_Fe | 3 (6.0%) | 3 (6.7%) | 12 (13%) | 0.4 | 0.5 |
| aSUP_Iod | 1 (2.0%) | 3 (6.7%) | 11 (12%) | 0.093 | 0.2 |
| aSUP_Ѡ3 | 6 (12%) | 14 (31%) | 47 (51%) | <0.001 | <0.001 |
| aSUP_CHLO | 0 (0%) | 1 (2.2%) | 0 (0%) | 0.2 | 0.4 |
| aSUP_ALG | 0 (0%) | 2 (4.4%) | 2 (2.2%) | 0.3 | 0.4 |
| aSUP_GB | 0 (0%) | 2 (4.4%) | 0 (0%) | 0.057 | 0.2 |
| aSUP_FORT | 1 (2.0%) | 3 (6.7%) | 2 (2.2%) | 0.4 | 0.6 |
| aSUP_PROB | 3 (6.0%) | 2 (4.4%) | 1 (1.1%) | 0.2 | 0.4 |
| aSUP_OTH | 15 (30%) | 14 (31%) | 23 (25%) | 0.7 | 0.8 |
| aUr_Krea | 6.2 (2.9, 13.8) | 5.8 (2.9, 12.2) | 4.9 (2.4, 11.0) | 0.5 | 0.6 |
| Unknown | 1 | 0 | 0 | ||
| aUr_Ca | 1.01 (0.57, 1.52) | 0.80 (0.40, 1.53) | 0.61 (0.26, 1.30) | 0.081 | 0.2 |
| Unknown | 1 | 0 | 0 | ||
| aCa_per_Krea | 0.17 (0.10, 0.25) | 0.18 (0.10, 0.25) | 0.14 (0.10, 0.21) | 0.4 | 0.6 |
| Unknown | 1 | 0 | 0 | ||
| aI_per_Krea | 181 (111, 328) | 109 (66, 243) | 144 (67, 254) | 0.11 | 0.3 |
| Unknown | 9 | 5 | 5 | ||
| aP_per_Krea | 1.71 (1.33, 2.17) | 1.46 (0.76, 2.00) | 1.15 (0.69, 1.52) | <0.001 | <0.001 |
| Unknown | 1 | 0 | 0 | ||
| aBREAKS | 27 (54%) | 23 (51%) | 37 (40%) | 0.2 | 0.4 |
| 1
Median (Q1, Q3); n (%) |
|||||
| 2
Kruskal-Wallis rank sum test; Pearson’s Chi-squared test; Fisher’s exact test |
|||||
| 3
False discovery rate correction for multiple testing |
|||||
Open code
DatChar_adult_df <- DatChar_adult$table_body %>%
as_tibble()2.2.4.2 OM vs VG
Open code
DatChar_adult_OM_VG <- run(
dat_adult %>%
select(-FAM, -ID) %>%
filter(GRP == 'OM' | GRP == 'VG') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(by = 'GRP') %>%
modify_caption("OM vs VG. Adults characteristics according to food preferences") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_adult_OM_VG', reuse=TRUE)
DatChar_adult_OM_VGCharacteristic |
OM |
VG |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 35.8 (32.8, 40.0) | 36.7 (33.4, 38.2) | >0.9 | >0.9 |
| SEX | >0.9 | >0.9 | ||
| F | 25 (50%) | 23 (51%) | ||
| M | 25 (50%) | 22 (49%) | ||
| aBMI | 24.5 (22.4, 26.7) | 22.9 (21.5, 26.1) | 0.3 | 0.6 |
| aWHR | 0.79 (0.75, 0.85) | 0.78 (0.73, 0.85) | >0.9 | >0.9 |
| aHEIGHT | 1.76 (1.69, 1.80) | 1.74 (1.72, 1.80) | 0.8 | >0.9 |
| aMASS | 75 (65, 84) | 72 (65, 80) | 0.8 | >0.9 |
| aHG | 38 (30, 54) | 43 (32, 51) | 0.6 | >0.9 |
| Unknown | 1 | 0 | ||
| aPFAT | 21 (18, 29) | 23 (16, 29) | >0.9 | >0.9 |
| aFAT | 17 (12, 22) | 17 (11, 23) | >0.9 | >0.9 |
| aFFM | 54 (48, 68) | 56 (49, 64) | 0.7 | >0.9 |
| aSBP | 125 (116, 140) | 121 (111, 134) | 0.3 | 0.6 |
| aDBP | 79 (70, 83) | 79 (73, 86) | 0.3 | 0.7 |
| aGLY | 4.49 (4.25, 4.77) | 4.44 (4.19, 4.66) | 0.4 | 0.8 |
| aTC | 4.85 (4.30, 5.40) | 4.28 (3.78, 5.02) | 0.005 | 0.076 |
| aHDL | 1.53 (1.23, 1.74) | 1.35 (1.20, 1.68) | 0.4 | 0.7 |
| aLDL | 2.81 (2.44, 3.34) | 2.36 (2.04, 3.10) | 0.016 | 0.14 |
| aTG | 0.87 (0.57, 1.16) | 0.76 (0.65, 1.02) | 0.4 | 0.8 |
| aCa | 2.44 (2.38, 2.52) | 2.45 (2.41, 2.50) | 0.5 | 0.8 |
| aP | 1.12 (1.06, 1.21) | 1.12 (0.97, 1.26) | >0.9 | >0.9 |
| aMg | 0.79 (0.77, 0.87) | 0.81 (0.78, 0.83) | >0.9 | >0.9 |
| aSe | 1.00 (0.92, 1.17) | 0.97 (0.67, 1.18) | 0.2 | 0.6 |
| aZn | 14.05 (12.90, 15.60) | 13.10 (11.70, 14.10) | 0.006 | 0.076 |
| aFE | 20 (16, 24) | 15 (12, 25) | 0.11 | 0.4 |
| aVKFE | 68 (62, 74) | 70 (62, 77) | 0.3 | 0.7 |
| aFERR | 38 (23, 83) | 25 (16, 50) | 0.025 | 0.2 |
| aTRF | 2.71 (2.46, 2.94) | 2.77 (2.46, 3.07) | 0.4 | 0.7 |
| aSATTRF | 28 (24, 36) | 22 (17, 39) | 0.076 | 0.3 |
| aTRFINDEX | 0.73 (0.61, 0.93) | 0.92 (0.64, 1.17) | 0.013 | 0.13 |
| Unknown | 0 | 1 | ||
| aSTRF | 1.18 (1.05, 1.32) | 1.25 (1.05, 1.47) | 0.10 | 0.4 |
| Unknown | 0 | 1 | ||
| aHGB | 147 (136, 154) | 144 (134, 154) | 0.4 | 0.8 |
| aMCV | 87.6 (86.0, 89.8) | 86.7 (85.1, 89.5) | 0.13 | 0.4 |
| aPTH | 2.95 (2.40, 4.00) | 3.00 (2.20, 3.40) | 0.5 | 0.8 |
| aCros | 0.36 (0.25, 0.56) | 0.36 (0.27, 0.48) | 0.6 | >0.9 |
| aP1NP | 45 (33, 60) | 43 (37, 61) | 0.4 | 0.8 |
| aUI | 120 (81, 213) | 94 (41, 171) | 0.091 | 0.4 |
| Unknown | 8 | 5 | ||
| aUREA | 4.80 (4.00, 5.70) | 4.40 (3.80, 5.10) | 0.2 | 0.5 |
| aCREA | 70 (59, 81) | 66 (58, 78) | 0.2 | 0.6 |
| aUA | 306 (249, 365) | 290 (246, 350) | 0.7 | >0.9 |
| aVIT_AKTB12 | 84 (71, 109) | 75 (54, 106) | 0.12 | 0.4 |
| aHCY | 15.2 (11.9, 18.1) | 15.8 (12.7, 21.5) | 0.4 | 0.7 |
| Unknown | 0 | 10 | ||
| aMMA | 194 (158, 234) | 236 (161, 305) | 0.050 | 0.3 |
| aVIT_D | 67 (51, 79) | 73 (59, 88) | 0.072 | 0.3 |
| aFOLAT | 9.2 (7.3, 11.6) | 12.9 (10.1, 15.4) | <0.001 | 0.012 |
| aAL_adult | 17 (34%) | 12 (27%) | 0.4 | 0.8 |
| aSUP_VEG1 | 0 (0%) | 6 (13%) | 0.009 | 0.11 |
| aSup_B12 | 1 (2.0%) | 23 (51%) | <0.001 | <0.001 |
| aSUP_FOL | 1 (2.0%) | 0 (0%) | >0.9 | >0.9 |
| aSUP_vitA | ||||
| 0 | 50 (100%) | 45 (100%) | ||
| aSUP_vitB1 | 1 (2.0%) | 1 (2.2%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 1 (2.0%) | 1 (2.2%) | >0.9 | >0.9 |
| aSUP_D | 17 (34%) | 34 (76%) | <0.001 | 0.002 |
| aSUP_Mg | 13 (26%) | 11 (24%) | 0.9 | >0.9 |
| aSUP_Zn | 6 (12%) | 6 (13%) | 0.8 | >0.9 |
| aSUP_Se | 0 (0%) | 1 (2.2%) | 0.5 | 0.8 |
| aSUP_Ca | 0 (0%) | 3 (6.7%) | 0.10 | 0.4 |
| aSUP_Fe | 3 (6.0%) | 3 (6.7%) | >0.9 | >0.9 |
| aSUP_Iod | 1 (2.0%) | 3 (6.7%) | 0.3 | 0.7 |
| aSUP_Ѡ3 | 6 (12%) | 14 (31%) | 0.023 | 0.2 |
| aSUP_CHLO | 0 (0%) | 1 (2.2%) | 0.5 | 0.8 |
| aSUP_ALG | 0 (0%) | 2 (4.4%) | 0.2 | 0.6 |
| aSUP_GB | 0 (0%) | 2 (4.4%) | 0.2 | 0.6 |
| aSUP_FORT | 1 (2.0%) | 3 (6.7%) | 0.3 | 0.7 |
| aSUP_PROB | 3 (6.0%) | 2 (4.4%) | >0.9 | >0.9 |
| aSUP_OTH | 15 (30%) | 14 (31%) | >0.9 | >0.9 |
| aUr_Krea | 6.2 (2.9, 13.8) | 5.8 (2.9, 12.2) | 0.8 | >0.9 |
| Unknown | 1 | 0 | ||
| aUr_Ca | 1.01 (0.57, 1.52) | 0.80 (0.40, 1.53) | 0.5 | 0.8 |
| Unknown | 1 | 0 | ||
| aCa_per_Krea | 0.17 (0.10, 0.25) | 0.18 (0.10, 0.25) | >0.9 | >0.9 |
| Unknown | 1 | 0 | ||
| aI_per_Krea | 181 (111, 328) | 109 (66, 243) | 0.046 | 0.3 |
| Unknown | 9 | 5 | ||
| aP_per_Krea | 1.71 (1.33, 2.17) | 1.46 (0.76, 2.00) | 0.074 | 0.3 |
| Unknown | 1 | 0 | ||
| aBREAKS | 27 (54%) | 23 (51%) | 0.8 | >0.9 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test; Wilcoxon rank sum exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.4.3 OM vs VN
Open code
DatChar_adult_OM_VN <- run(
dat_adult %>%
select(-FAM, -ID) %>%
filter(GRP == 'OM' | GRP == 'VN') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(by = 'GRP') %>%
modify_caption("OM vs VN. Adults characteristics according to food preferences") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_adult_OM_VN', reuse=TRUE)
DatChar_adult_OM_VNCharacteristic |
OM |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 35.8 (32.8, 40.0) | 33.9 (31.5, 37.2) | 0.035 | 0.11 |
| SEX | >0.9 | >0.9 | ||
| F | 25 (50%) | 47 (51%) | ||
| M | 25 (50%) | 45 (49%) | ||
| aBMI | 24.5 (22.4, 26.7) | 22.6 (20.8, 25.6) | 0.020 | 0.080 |
| aWHR | 0.79 (0.75, 0.85) | 0.78 (0.73, 0.82) | 0.2 | 0.4 |
| Unknown | 0 | 4 | ||
| aHEIGHT | 1.76 (1.69, 1.80) | 1.73 (1.66, 1.81) | 0.5 | 0.7 |
| aMASS | 75 (65, 84) | 69 (59, 81) | 0.078 | 0.2 |
| aHG | 38 (30, 54) | 40 (31, 52) | 0.8 | >0.9 |
| Unknown | 1 | 0 | ||
| aPFAT | 21 (18, 29) | 21 (15, 26) | 0.2 | 0.4 |
| aFAT | 17 (12, 22) | 14 (10, 18) | 0.039 | 0.11 |
| aFFM | 54 (48, 68) | 53 (45, 65) | 0.2 | 0.4 |
| aSBP | 125 (116, 140) | 121 (112, 134) | 0.083 | 0.2 |
| aDBP | 79 (70, 83) | 75 (70, 80) | 0.11 | 0.2 |
| aGLY | 4.49 (4.25, 4.77) | 4.45 (4.13, 4.71) | 0.2 | 0.4 |
| aTC | 4.85 (4.30, 5.40) | 4.15 (3.65, 4.68) | <0.001 | <0.001 |
| aHDL | 1.53 (1.23, 1.74) | 1.43 (1.24, 1.69) | 0.5 | 0.7 |
| aLDL | 2.81 (2.44, 3.34) | 2.23 (1.92, 2.77) | <0.001 | <0.001 |
| aTG | 0.87 (0.57, 1.16) | 0.74 (0.57, 1.06) | 0.2 | 0.4 |
| aCa | 2.44 (2.38, 2.52) | 2.46 (2.42, 2.51) | 0.5 | 0.7 |
| aP | 1.12 (1.06, 1.21) | 1.08 (1.01, 1.21) | 0.2 | 0.4 |
| aMg | 0.79 (0.77, 0.87) | 0.81 (0.77, 0.85) | >0.9 | >0.9 |
| aSe | 1.00 (0.92, 1.17) | 0.97 (0.75, 1.18) | 0.2 | 0.4 |
| aZn | 14.05 (12.90, 15.60) | 12.10 (10.75, 13.80) | <0.001 | <0.001 |
| aFE | 20 (16, 24) | 19 (15, 25) | >0.9 | >0.9 |
| aVKFE | 68 (62, 74) | 68 (65, 76) | 0.5 | 0.6 |
| aFERR | 38 (23, 83) | 26 (14, 35) | <0.001 | 0.005 |
| aTRF | 2.71 (2.46, 2.94) | 2.70 (2.56, 3.02) | 0.5 | 0.6 |
| aSATTRF | 28 (24, 36) | 29 (21, 36) | 0.8 | >0.9 |
| aTRFINDEX | 0.73 (0.61, 0.93) | 0.84 (0.70, 1.02) | 0.010 | 0.047 |
| Unknown | 0 | 1 | ||
| aSTRF | 1.18 (1.05, 1.32) | 1.21 (1.01, 1.34) | 0.6 | 0.7 |
| aHGB | 147 (136, 154) | 145 (135, 156) | 0.7 | 0.8 |
| aMCV | 87.6 (86.0, 89.8) | 89.7 (87.0, 91.8) | 0.019 | 0.080 |
| aPTH | 2.95 (2.40, 4.00) | 3.30 (2.70, 4.10) | 0.063 | 0.2 |
| aCros | 0.36 (0.25, 0.56) | 0.41 (0.30, 0.59) | 0.3 | 0.4 |
| aP1NP | 45 (33, 60) | 52 (40, 73) | 0.026 | 0.093 |
| aUI | 120 (81, 213) | 91 (45, 152) | 0.033 | 0.11 |
| Unknown | 8 | 5 | ||
| aUREA | 4.80 (4.00, 5.70) | 3.95 (3.20, 4.50) | <0.001 | <0.001 |
| aCREA | 70 (59, 81) | 64 (56, 72) | 0.009 | 0.046 |
| aUA | 306 (249, 365) | 300 (247, 348) | 0.7 | 0.8 |
| aVIT_AKTB12 | 84 (71, 109) | 90 (66, 124) | 0.6 | 0.7 |
| aHCY | 15.2 (11.9, 18.1) | 14.2 (12.5, 17.1) | 0.4 | 0.6 |
| Unknown | 0 | 14 | ||
| aMMA | 194 (158, 234) | 170 (134, 215) | 0.024 | 0.089 |
| aVIT_D | 67 (51, 79) | 76 (65, 92) | <0.001 | 0.003 |
| aFOLAT | 9.2 (7.3, 11.6) | 12.6 (9.7, 16.2) | <0.001 | <0.001 |
| aAL_adult | 17 (34%) | 12 (13%) | 0.003 | 0.018 |
| aSUP_VEG1 | 0 (0%) | 4 (4.3%) | 0.3 | 0.4 |
| aSup_B12 | 1 (2.0%) | 76 (83%) | <0.001 | <0.001 |
| aSUP_FOL | 1 (2.0%) | 6 (6.5%) | 0.4 | 0.6 |
| aSUP_vitA | 0 (0%) | 2 (2.2%) | 0.5 | 0.7 |
| aSUP_vitB1 | 1 (2.0%) | 2 (2.2%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 1 (2.0%) | 2 (2.2%) | >0.9 | >0.9 |
| aSUP_D | 17 (34%) | 65 (71%) | <0.001 | <0.001 |
| aSUP_Mg | 13 (26%) | 12 (13%) | 0.053 | 0.15 |
| aSUP_Zn | 6 (12%) | 5 (5.4%) | 0.2 | 0.4 |
| aSUP_Se | 0 (0%) | 3 (3.3%) | 0.6 | 0.7 |
| aSUP_Ca | 0 (0%) | 10 (11%) | 0.015 | 0.066 |
| aSUP_Fe | 3 (6.0%) | 12 (13%) | 0.2 | 0.4 |
| aSUP_Iod | 1 (2.0%) | 11 (12%) | 0.056 | 0.2 |
| aSUP_Ѡ3 | 6 (12%) | 47 (51%) | <0.001 | <0.001 |
| aSUP_CHLO | ||||
| 0 | 50 (100%) | 92 (100%) | ||
| aSUP_ALG | 0 (0%) | 2 (2.2%) | 0.5 | 0.7 |
| aSUP_GB | ||||
| 0 | 50 (100%) | 92 (100%) | ||
| aSUP_FORT | 1 (2.0%) | 2 (2.2%) | >0.9 | >0.9 |
| aSUP_PROB | 3 (6.0%) | 1 (1.1%) | 0.13 | 0.3 |
| aSUP_OTH | 15 (30%) | 23 (25%) | 0.5 | 0.7 |
| aUr_Krea | 6.2 (2.9, 13.8) | 4.9 (2.4, 11.0) | 0.3 | 0.4 |
| Unknown | 1 | 0 | ||
| aUr_Ca | 1.01 (0.57, 1.52) | 0.61 (0.26, 1.30) | 0.035 | 0.11 |
| Unknown | 1 | 0 | ||
| aCa_per_Krea | 0.17 (0.10, 0.25) | 0.14 (0.10, 0.21) | 0.3 | 0.4 |
| Unknown | 1 | 0 | ||
| aI_per_Krea | 181 (111, 328) | 144 (67, 254) | 0.11 | 0.2 |
| Unknown | 9 | 5 | ||
| aP_per_Krea | 1.71 (1.33, 2.17) | 1.15 (0.69, 1.52) | <0.001 | <0.001 |
| Unknown | 1 | 0 | ||
| aBREAKS | 27 (54%) | 37 (40%) | 0.11 | 0.3 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.2.4.4 VG vs VN
Open code
DatChar_adult_VG_VN <- run(
dat_adult %>%
select(-FAM, -ID) %>%
filter(GRP == 'VG' | GRP == 'VN') %>%
mutate(GRP = factor(GRP)) %>%
tbl_summary(by = 'GRP') %>%
modify_caption("VG vs VN. Adults characteristics according to food preferences") %>%
add_p() %>%
add_q() %>%
as_gt(),
path = 'gitignore/run/DatChar_adult_VG_VN', reuse=TRUE)
DatChar_adult_VG_VNCharacteristic |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|
| aAGE | 36.7 (33.4, 38.2) | 33.9 (31.5, 37.2) | 0.018 | 0.2 |
| SEX | >0.9 | >0.9 | ||
| F | 23 (51%) | 47 (51%) | ||
| M | 22 (49%) | 45 (49%) | ||
| aBMI | 22.9 (21.5, 26.1) | 22.6 (20.8, 25.6) | 0.3 | 0.6 |
| aWHR | 0.78 (0.73, 0.85) | 0.78 (0.73, 0.82) | 0.3 | 0.6 |
| Unknown | 0 | 4 | ||
| aHEIGHT | 1.74 (1.72, 1.80) | 1.73 (1.66, 1.81) | 0.3 | 0.6 |
| aMASS | 72 (65, 80) | 69 (59, 81) | 0.14 | 0.4 |
| aHG | 43 (32, 51) | 40 (31, 52) | 0.7 | 0.8 |
| aPFAT | 23 (16, 29) | 21 (15, 26) | 0.3 | 0.6 |
| aFAT | 17 (11, 23) | 14 (10, 18) | 0.11 | 0.4 |
| aFFM | 56 (49, 64) | 53 (45, 65) | 0.4 | 0.6 |
| aSBP | 121 (111, 134) | 121 (112, 134) | 0.8 | >0.9 |
| aDBP | 79 (73, 86) | 75 (70, 80) | 0.005 | 0.081 |
| aGLY | 4.44 (4.19, 4.66) | 4.45 (4.13, 4.71) | >0.9 | >0.9 |
| aTC | 4.28 (3.78, 5.02) | 4.15 (3.65, 4.68) | 0.2 | 0.4 |
| aHDL | 1.35 (1.20, 1.68) | 1.43 (1.24, 1.69) | 0.6 | 0.8 |
| aLDL | 2.36 (2.04, 3.10) | 2.23 (1.92, 2.77) | 0.11 | 0.4 |
| aTG | 0.76 (0.65, 1.02) | 0.74 (0.57, 1.06) | 0.5 | 0.8 |
| aCa | 2.45 (2.41, 2.50) | 2.46 (2.42, 2.51) | >0.9 | >0.9 |
| aP | 1.12 (0.97, 1.26) | 1.08 (1.01, 1.21) | 0.4 | 0.6 |
| aMg | 0.81 (0.78, 0.83) | 0.81 (0.77, 0.85) | 0.8 | >0.9 |
| aSe | 0.97 (0.67, 1.18) | 0.97 (0.75, 1.18) | >0.9 | >0.9 |
| aZn | 13.10 (11.70, 14.10) | 12.10 (10.75, 13.80) | 0.032 | 0.2 |
| aFE | 15 (12, 25) | 19 (15, 25) | 0.082 | 0.4 |
| aVKFE | 70 (62, 77) | 68 (65, 76) | 0.8 | >0.9 |
| aFERR | 25 (16, 50) | 26 (14, 35) | 0.4 | 0.6 |
| aTRF | 2.77 (2.46, 3.07) | 2.70 (2.56, 3.02) | 0.8 | >0.9 |
| aSATTRF | 22 (17, 39) | 29 (21, 36) | 0.090 | 0.4 |
| aTRFINDEX | 0.92 (0.64, 1.17) | 0.84 (0.70, 1.02) | 0.6 | 0.8 |
| Unknown | 1 | 1 | ||
| aSTRF | 1.25 (1.05, 1.47) | 1.21 (1.01, 1.34) | 0.2 | 0.4 |
| Unknown | 1 | 0 | ||
| aHGB | 144 (134, 154) | 145 (135, 156) | 0.7 | >0.9 |
| aMCV | 86.7 (85.1, 89.5) | 89.7 (87.0, 91.8) | <0.001 | 0.012 |
| aPTH | 3.00 (2.20, 3.40) | 3.30 (2.70, 4.10) | 0.014 | 0.2 |
| aCros | 0.36 (0.27, 0.48) | 0.41 (0.30, 0.59) | 0.095 | 0.4 |
| aP1NP | 43 (37, 61) | 52 (40, 73) | 0.2 | 0.4 |
| aUI | 94 (41, 171) | 91 (45, 152) | >0.9 | >0.9 |
| Unknown | 5 | 5 | ||
| aUREA | 4.40 (3.80, 5.10) | 3.95 (3.20, 4.50) | 0.007 | 0.10 |
| aCREA | 66 (58, 78) | 64 (56, 72) | 0.3 | 0.6 |
| aUA | 290 (246, 350) | 300 (247, 348) | 0.8 | >0.9 |
| aVIT_AKTB12 | 75 (54, 106) | 90 (66, 124) | 0.036 | 0.3 |
| aHCY | 15.8 (12.7, 21.5) | 14.2 (12.5, 17.1) | 0.067 | 0.4 |
| Unknown | 10 | 14 | ||
| aMMA | 236 (161, 305) | 170 (134, 215) | <0.001 | 0.014 |
| aVIT_D | 73 (59, 88) | 76 (65, 92) | 0.12 | 0.4 |
| aFOLAT | 12.9 (10.1, 15.4) | 12.6 (9.7, 16.2) | 0.8 | >0.9 |
| aAL_adult | 12 (27%) | 12 (13%) | 0.049 | 0.3 |
| aSUP_VEG1 | 6 (13%) | 4 (4.3%) | 0.080 | 0.4 |
| aSup_B12 | 23 (51%) | 76 (83%) | <0.001 | 0.008 |
| aSUP_FOL | 0 (0%) | 6 (6.5%) | 0.2 | 0.4 |
| aSUP_vitA | 0 (0%) | 2 (2.2%) | >0.9 | >0.9 |
| aSUP_vitB1 | 1 (2.2%) | 2 (2.2%) | >0.9 | >0.9 |
| aSUP_vit.B5 | 1 (2.2%) | 2 (2.2%) | >0.9 | >0.9 |
| aSUP_D | 34 (76%) | 65 (71%) | 0.5 | 0.8 |
| aSUP_Mg | 11 (24%) | 12 (13%) | 0.094 | 0.4 |
| aSUP_Zn | 6 (13%) | 5 (5.4%) | 0.2 | 0.4 |
| aSUP_Se | 1 (2.2%) | 3 (3.3%) | >0.9 | >0.9 |
| aSUP_Ca | 3 (6.7%) | 10 (11%) | 0.5 | 0.8 |
| aSUP_Fe | 3 (6.7%) | 12 (13%) | 0.4 | 0.6 |
| aSUP_Iod | 3 (6.7%) | 11 (12%) | 0.5 | 0.8 |
| aSUP_Ѡ3 | 14 (31%) | 47 (51%) | 0.027 | 0.2 |
| aSUP_CHLO | 1 (2.2%) | 0 (0%) | 0.3 | 0.6 |
| aSUP_ALG | 2 (4.4%) | 2 (2.2%) | 0.6 | 0.8 |
| aSUP_GB | 2 (4.4%) | 0 (0%) | 0.11 | 0.4 |
| aSUP_FORT | 3 (6.7%) | 2 (2.2%) | 0.3 | 0.6 |
| aSUP_PROB | 2 (4.4%) | 1 (1.1%) | 0.3 | 0.6 |
| aSUP_OTH | 14 (31%) | 23 (25%) | 0.4 | 0.7 |
| aUr_Krea | 5.8 (2.9, 12.2) | 4.9 (2.4, 11.0) | 0.4 | 0.6 |
| aUr_Ca | 0.80 (0.40, 1.53) | 0.61 (0.26, 1.30) | 0.2 | 0.4 |
| aCa_per_Krea | 0.18 (0.10, 0.25) | 0.14 (0.10, 0.21) | 0.3 | 0.6 |
| aI_per_Krea | 109 (66, 243) | 144 (67, 254) | 0.5 | 0.7 |
| Unknown | 5 | 5 | ||
| aP_per_Krea | 1.46 (0.76, 2.00) | 1.15 (0.69, 1.52) | 0.044 | 0.3 |
| aBREAKS | 23 (51%) | 37 (40%) | 0.2 | 0.5 |
| 1
Median (Q1, Q3); n (%) |
||||
| 2
Wilcoxon rank sum test; Pearson’s Chi-squared test; Fisher’s exact test |
||||
| 3
False discovery rate correction for multiple testing |
||||
2.3 Distribution of numerical characteristics
2.3.1 All children histograms
Open code
## Reshaping the data to long format
dat_long <- dat_child_all
dat_long <- dat_long %>%
select(where(~is.numeric(.) && length(unique(.)) >3)) %>%
pivot_longer(cols = everything(), names_to = "variable", values_to = "value") %>%
mutate(variable = factor(variable, levels = names(dat_long)))
# Creating the histogram matrix
ggplot(dat_long, aes(x = value)) +
geom_histogram(bins = 20, fill = "skyblue2", color = "grey60") +
facet_wrap(~ variable, scales = "free") +
labs(x = "Value", y = "Count", title = "Histogram of Numerical Variables, all children")2.3.2 Young children histograms
Open code
## Reshaping the data to long format
dat_long <- dat_child_young
dat_long <- dat_long %>%
select(where(~is.numeric(.) && length(unique(.)) >3)) %>%
pivot_longer(cols = everything(), names_to = "variable", values_to = "value") %>%
mutate(variable = factor(variable, levels = names(dat_long)))
# Creating the histogram matrix
ggplot(dat_long, aes(x = value)) +
geom_histogram(bins = 20, fill = "skyblue2", color = "grey60") +
facet_wrap(~ variable, scales = "free") +
labs(x = "Value", y = "Count", title = "Histogram of Numerical Variables, young children")2.3.3 Old children histograms
Open code
## Reshaping the data to long format
dat_long <- dat_child_old
dat_long <- dat_long %>%
select(where(~is.numeric(.) && length(unique(.)) >3)) %>%
pivot_longer(cols = everything(), names_to = "variable", values_to = "value") %>%
mutate(variable = factor(variable, levels = names(dat_long)))
# Creating the histogram matrix
ggplot(dat_long, aes(x = value)) +
geom_histogram(bins = 20, fill = "skyblue2", color = "grey60") +
facet_wrap(~ variable, scales = "free") +
labs(x = "Value", y = "Count", title = "Histogram of Numerical Variables, old children")2.3.4 Adults histograms
Open code
## Reshaping the data to long format
dat_long <- dat_adult
dat_long <- dat_long %>%
select(where(~is.numeric(.) && length(unique(.)) >3)) %>%
pivot_longer(cols = everything(), names_to = "variable", values_to = "value") %>%
mutate(variable = factor(variable, levels = names(dat_long)))
# Creating the histogram matrix
ggplot(dat_long, aes(x = value)) +
geom_histogram(bins = 20, fill = "skyblue2", color = "grey61") +
facet_wrap(~ variable, scales = "free") +
labs(x = "Value", y = "Count", title = "Histogram of Numerical Variables, adults ")2.4 Plot of group characteristics
2.4.1 All children
Open code
## define color
colo <- c('#F9FFAF', '#ACE1A3', '#329243')
## prepare data
df <- dat_child_all
tr <- DatChar_child_all_df %>%
filter(!is.na(q.value)) %>%
select(variable, q.value)
df <- df %>%
select(where(~is.numeric(.) && length(unique(.)) >3) | GRP)
## define outcomes of interest
outcomes <- data.frame(
variable = setdiff(names(df), c(
'GRP',
'log2_age',
'aBreastFeed_full_duration')))
outcomes <- outcomes %>%
inner_join(tr, by = 'variable')
## define comparison
my_comparisons <- list( c('OM', 'VG'), c('OM', 'VN'), c('VG', 'VN') )
## function to boxplot
boxplot_cond <- function(variable, q.value) {
clean_data <- df %>%
select(GRP, all_of(variable)) %>%
drop_na()
upper_limit <- max(clean_data[[variable]], na.rm = TRUE) * 1.5
p <- ggboxplot(clean_data,
x = 'GRP',
y = variable,
fill = 'GRP',
tip.length = 0.15,
palette = colo,
outlier.shape = 1,
lwd = 0.25,
outlier.size = 0.8) +
theme(
plot.title = element_text(size = 10), # Smaller title
axis.title = element_text(size = 8), # Smaller axis titles
axis.text = element_text(size = 7) # Smaller axis labels
) +
rremove("legend") +
coord_cartesian(ylim = c(0, upper_limit))
if (q.value < 0.05) {
p <- p + stat_compare_means(
method = 'wilcox.test',
label = 'P',
comparisons = my_comparisons,
size = 3,
label.y = upper_limit * c(0.7, 0.8, 0.9))
}
return(p)
}
# Plot all outcomes
plots <- pmap(outcomes, boxplot_cond)
# Arrange plots in a matrix
plots_arranged <- ggarrange(plotlist = plots, ncol = 8, nrow = 5)
plots_arranged
## $`1`##
## $`2`
##
## attr(,"class")
## [1] "list" "ggarrange"
2.4.2 Young children
Open code
## data
df <- dat_child_young
df <- df %>%
select(where(~is.numeric(.) && length(unique(.)) >3) | GRP)
## defining outcomes of interest
tr <- DatChar_child_young_df %>%
filter(!is.na(q.value)) %>%
select(variable, q.value)
df <- df %>%
select(where(~is.numeric(.) && length(unique(.)) >3) | GRP)
## define outcomes of interest
outcomes <- data.frame(
variable = setdiff(names(df), c(
'GRP',
'log2_age',
'aBreastFeed_full_duration')))
outcomes <- outcomes %>%
inner_join(tr, by = 'variable')
## plot all outcomes
plots <- pmap(outcomes, boxplot_cond)
## matrix of plot
plots_arranged <- ggarrange(plotlist = plots, ncol = 9, nrow = 5)
plots_arranged2.4.3 Old children
Open code
## data
df <- dat_child_old
df <- df %>%
select(where(~is.numeric(.) && length(unique(.)) >3) | GRP)
## defining outcomes of interest
tr <- DatChar_child_old_df %>%
filter(!is.na(q.value)) %>%
select(variable, q.value)
df <- df %>%
select(where(~is.numeric(.) && length(unique(.)) >3) | GRP)
## define outcomes of interest
outcomes <- data.frame(
variable = setdiff(names(df), c(
'GRP',
'log2_age',
'aBreastFeed_full_duration')))
outcomes <- outcomes %>%
inner_join(tr, by = 'variable')
## plot all outcomes
plots <- pmap(outcomes, boxplot_cond)
## matrix of plot
plots_arranged <- ggarrange(plotlist = plots, ncol = 9, nrow = 5)
plots_arranged2.4.4 Adults
Open code
## data
df <- dat_adult
df <- df %>%
select(where(~is.numeric(.) && length(unique(.)) >3) | GRP) %>%
select(-aCros)
## defining outcomes of interest
tr <- DatChar_adult_df %>%
filter(!is.na(q.value)) %>%
select(variable, q.value)
df <- df %>%
select(where(~is.numeric(.) && length(unique(.)) >3) | GRP)
## define outcomes of interest
outcomes <- data.frame(
variable = setdiff(names(df), c(
'GRP',
'log2_age')))
outcomes <- outcomes %>%
inner_join(tr, by = 'variable')
## plot all outcomes
plots <- pmap(outcomes, boxplot_cond)
## matrix of plot
plots_arranged <- ggarrange(plotlist = plots, ncol = 8, nrow = 6)
plots_arranged3 Food intake summary
Open code
dat_food %>% summary()
## GRP Calories.kcal. Carbohydrates.g. Fat.g. Proteins.g.
## OM: 71 Min. : 488.5 Min. : 49.6 Min. : 12.94 Min. : 8.967
## VG: 61 1st Qu.:1175.6 1st Qu.:142.9 1st Qu.: 39.76 1st Qu.: 37.557
## VN:135 Median :1738.4 Median :200.8 Median : 59.48 Median : 59.423
## Mean :1790.5 Mean :210.1 Mean : 64.12 Mean : 63.414
## 3rd Qu.:2310.7 3rd Qu.:268.1 3rd Qu.: 82.02 3rd Qu.: 83.641
## Max. :4219.1 Max. :566.7 Max. :178.78 Max. :177.875
##
## Fiber.g. Sugars.g. Saturated.fats..SAFA..g. Cholesterol.mg.
## Min. : 0.00 Min. : 10.07 Min. : 0.03763 Min. : 0.0000
## 1st Qu.:14.71 1st Qu.: 45.94 1st Qu.: 8.62974 1st Qu.: 0.0684
## Median :23.73 Median : 60.14 Median :14.02014 Median : 30.8760
## Mean :27.13 Mean : 66.07 Mean :17.20864 Mean : 64.0970
## 3rd Qu.:35.63 3rd Qu.: 79.80 3rd Qu.:24.52420 3rd Qu.:102.1615
## Max. :95.39 Max. :188.59 Max. :60.13940 Max. :432.7600
## NA's :7
## Phosphorus.mg. Magnesium.mg. Zinc.mg. Selenium.μg.
## Min. : 103.3 Min. : 20.67 Min. : 0.7287 Min. : 1.38
## 1st Qu.: 529.1 1st Qu.: 150.26 1st Qu.: 3.9645 1st Qu.:10.68
## Median : 816.2 Median : 263.16 Median : 6.6042 Median :19.15
## Mean : 915.8 Mean : 300.69 Mean : 8.3542 Mean :23.06
## 3rd Qu.:1272.5 3rd Qu.: 401.73 3rd Qu.:10.6941 3rd Qu.:31.20
## Max. :3210.3 Max. :1031.60 Max. :45.5507 Max. :91.06
##
## Iron.mg. Calcium.mg. Iodine.μg. Age_category
## Min. : 0.4823 Min. : 66.8 Min. : 4.152 Adult :154
## 1st Qu.: 4.5585 1st Qu.: 375.3 1st Qu.: 36.167 Ch < 3 yrs: 65
## Median : 8.2290 Median : 588.6 Median : 53.672 Ch > 3 yrs: 48
## Mean : 9.2992 Mean : 664.2 Mean : 57.135
## 3rd Qu.:12.0101 3rd Qu.: 874.1 3rd Qu.: 68.933
## Max. :33.1056 Max. :2095.8 Max. :323.739
## 3.1 Summary tables
3.1.1 Children all
Open code
food_int_child_all <- run(
dat_food %>%
filter(Age_category != 'Adult') %>%
select(-Age_category) %>%
tbl_summary(
by = 'GRP') %>%
modify_caption("Nutrients intake in children (all)") %>%
add_p() %>%
add_q(),
path = 'gitignore/run/food_int_child_all', reuse = TRUE)
food_int_child_allCharacteristic |
OM |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|---|
| Calories.kcal. | 1,047 (831, 1,386) | 1,108 (967, 1,449) | 1,083 (906, 1,370) | 0.7 | 0.8 |
| Carbohydrates.g. | 121 (107, 158) | 142 (102, 188) | 135 (101, 185) | 0.4 | 0.6 |
| Fat.g. | 38 (33, 51) | 44 (34, 51) | 38 (31, 48) | 0.6 | 0.7 |
| Proteins.g. | 38 (29, 51) | 36 (28, 49) | 32 (22, 42) | 0.028 | 0.084 |
| Fiber.g. | 12 (7, 15) | 16 (11, 22) | 16 (9, 26) | 0.011 | 0.042 |
| Sugars.g. | 59 (46, 78) | 48 (39, 67) | 58 (45, 70) | 0.3 | 0.5 |
| Saturated.fats..SAFA..g. | 15 (9, 20) | 10 (6, 19) | 5 (4, 8) | <0.001 | <0.001 |
| Unknown | 1 | 1 | 5 | ||
| Cholesterol.mg. | 101 (64, 130) | 78 (23, 98) | 7 (0, 83) | <0.001 | <0.001 |
| Phosphorus.mg. | 598 (359, 751) | 518 (296, 762) | 396 (238, 672) | 0.10 | 0.2 |
| Magnesium.mg. | 136 (85, 169) | 144 (72, 204) | 141 (91, 239) | 0.6 | 0.7 |
| Zinc.mg. | 3.98 (2.74, 5.38) | 3.47 (2.59, 5.35) | 4.40 (2.72, 6.71) | 0.6 | 0.7 |
| Selenium.μg. | 17 (11, 22) | 11 (8, 22) | 9 (8, 12) | <0.001 | 0.005 |
| Iron.mg. | 3.77 (2.20, 5.61) | 4.37 (1.69, 5.69) | 4.52 (2.79, 6.99) | 0.8 | 0.8 |
| Calcium.mg. | 417 (296, 598) | 427 (279, 546) | 338 (271, 402) | 0.2 | 0.3 |
| Iodine.μg. | 47 (26, 57) | 46 (24, 56) | 37 (20, 52) | 0.3 | 0.5 |
| 1
Median (Q1, Q3) |
|||||
| 2
Kruskal-Wallis rank sum test |
|||||
| 3
False discovery rate correction for multiple testing |
|||||
Open code
food_int_child_all_df <- food_int_child_all$table_body %>%
as_tibble()3.1.2 Children young
Open code
food_int_child_young <- run(
dat_food %>%
filter(Age_category == 'Ch < 3 yrs') %>%
select(-Age_category) %>%
tbl_summary(
by = 'GRP') %>%
modify_caption("Nutrients intake in children < 3 years of age") %>%
add_p() %>%
add_q(),
path = 'gitignore/run/food_int_child_young', reuse = TRUE)
food_int_child_youngCharacteristic |
OM |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|---|
| Calories.kcal. | 856 (750, 1,027) | 980 (780, 1,088) | 1,008 (665, 1,349) | 0.5 | 0.7 |
| Carbohydrates.g. | 104 (89, 116) | 119 (82, 149) | 122 (85, 168) | 0.3 | 0.7 |
| Fat.g. | 36 (22, 40) | 37 (32, 47) | 38 (30, 48) | 0.4 | 0.7 |
| Proteins.g. | 29 (21, 36) | 29 (19, 35) | 30 (16, 37) | 0.9 | 0.9 |
| Fiber.g. | 8 (4, 12) | 12 (5, 17) | 15 (8, 19) | 0.074 | 0.3 |
| Sugars.g. | 51 (43, 64) | 58 (44, 78) | 60 (49, 75) | 0.5 | 0.7 |
| Saturated.fats..SAFA..g. | 9.5 (5.8, 15.3) | 5.2 (2.2, 8.9) | 5.2 (3.1, 8.0) | 0.032 | 0.3 |
| Unknown | 1 | 1 | 5 | ||
| Cholesterol.mg. | 101 (52, 121) | 91 (42, 120) | 52 (0, 103) | 0.037 | 0.3 |
| Phosphorus.mg. | 345 (298, 573) | 313 (188, 523) | 357 (209, 584) | 0.7 | 0.8 |
| Magnesium.mg. | 90 (58, 146) | 90 (53, 147) | 124 (76, 191) | 0.5 | 0.7 |
| Zinc.mg. | 2.90 (2.34, 4.34) | 2.86 (2.43, 4.89) | 4.36 (2.64, 5.84) | 0.2 | 0.5 |
| Selenium.μg. | 12.0 (9.7, 17.1) | 8.4 (7.6, 18.8) | 8.9 (7.7, 11.2) | 0.057 | 0.3 |
| Iron.mg. | 2.33 (1.35, 3.68) | 2.64 (1.30, 4.65) | 3.69 (1.81, 5.42) | 0.3 | 0.7 |
| Calcium.mg. | 337 (290, 541) | 286 (271, 388) | 337 (271, 401) | 0.6 | 0.7 |
| Iodine.μg. | 50 (27, 58) | 50 (31, 53) | 42 (29, 52) | 0.6 | 0.7 |
| 1
Median (Q1, Q3) |
|||||
| 2
Kruskal-Wallis rank sum test |
|||||
| 3
False discovery rate correction for multiple testing |
|||||
Open code
food_int_child_young_df <- food_int_child_young$table_body %>%
as_tibble()3.1.3 Children old
Open code
food_int_child_old <- run(
dat_food %>%
filter(Age_category == 'Ch > 3 yrs') %>%
select(-Age_category) %>%
tbl_summary(
by = 'GRP') %>%
modify_caption("Nutrients intake in children of 3+ years of age") %>%
add_p() %>%
add_q(),
path = 'gitignore/run/food_int_child_old', reuse = TRUE)
food_int_child_oldCharacteristic |
OM |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|---|
| Calories.kcal. | 1,386 (1,132, 1,690) | 1,369 (1,108, 1,657) | 1,250 (1,080, 1,425) | 0.6 | 0.6 |
| Carbohydrates.g. | 158 (135, 179) | 166 (123, 222) | 172 (140, 196) | 0.6 | 0.6 |
| Fat.g. | 51 (36, 66) | 47 (38, 53) | 39 (36, 42) | 0.4 | 0.5 |
| Proteins.g. | 50 (46, 60) | 42 (35, 59) | 42 (29, 45) | 0.041 | 0.12 |
| Fiber.g. | 14 (14, 16) | 19 (12, 23) | 26 (17, 31) | 0.003 | 0.016 |
| Sugars.g. | 71 (50, 89) | 45 (38, 61) | 54 (45, 66) | 0.049 | 0.12 |
| Saturated.fats..SAFA..g. | 20 (16, 26) | 14 (11, 21) | 7 (5, 10) | <0.001 | <0.001 |
| Cholesterol.mg. | 111 (77, 163) | 53 (1, 84) | 0 (0, 0) | <0.001 | <0.001 |
| Phosphorus.mg. | 637 (598, 892) | 667 (428, 817) | 541 (390, 776) | 0.3 | 0.4 |
| Magnesium.mg. | 163 (129, 185) | 156 (140, 214) | 239 (164, 328) | 0.077 | 0.2 |
| Zinc.mg. | 4.65 (3.83, 6.53) | 3.53 (3.00, 5.35) | 4.81 (2.92, 7.55) | 0.4 | 0.5 |
| Selenium.μg. | 20 (16, 33) | 14 (9, 28) | 10 (8, 17) | 0.021 | 0.078 |
| Iron.mg. | 5.61 (5.12, 7.33) | 5.22 (4.35, 6.82) | 6.23 (4.76, 8.75) | 0.4 | 0.5 |
| Calcium.mg. | 495 (309, 662) | 476 (420, 601) | 346 (327, 502) | 0.2 | 0.4 |
| Iodine.μg. | 38 (24, 54) | 38 (22, 58) | 21 (14, 39) | 0.14 | 0.3 |
| 1
Median (Q1, Q3) |
|||||
| 2
Kruskal-Wallis rank sum test |
|||||
| 3
False discovery rate correction for multiple testing |
|||||
Open code
food_int_child_old_df <- food_int_child_old$table_body %>%
as_tibble()3.1.4 Adults
Open code
food_int_adult <- run(
dat_food %>%
filter(Age_category == 'Adult') %>%
select(-Age_category) %>%
tbl_summary(
by = 'GRP') %>%
modify_caption("Nutrients intake in adults") %>%
add_p() %>%
add_q(),
path = 'gitignore/run/food_int_adult', reuse = TRUE)
food_int_adultCharacteristic |
OM |
VG |
VN |
p-value 2 |
q-value 3 |
|---|---|---|---|---|---|
| Calories.kcal. | 2,029 (1,698, 2,381) | 2,246 (1,701, 2,669) | 2,247 (1,844, 2,773) | 0.2 | 0.2 |
| Carbohydrates.g. | 214 (178, 248) | 221 (199, 289) | 284 (228, 337) | <0.001 | <0.001 |
| Fat.g. | 77 (59, 92) | 77 (64, 100) | 72 (60, 95) | >0.9 | >0.9 |
| Proteins.g. | 84 (73, 106) | 70 (59, 104) | 75 (65, 97) | 0.3 | 0.3 |
| Fiber.g. | 20 (16, 26) | 32 (22, 42) | 38 (30, 52) | <0.001 | <0.001 |
| Sugars.g. | 62 (46, 88) | 63 (44, 102) | 65 (50, 81) | 0.9 | >0.9 |
| Saturated.fats..SAFA..g. | 30 (23, 37) | 23 (14, 31) | 14 (10, 19) | <0.001 | <0.001 |
| Cholesterol.mg. | 164 (135, 232) | 56 (6, 83) | 0 (0, 1) | <0.001 | <0.001 |
| Phosphorus.mg. | 1,186 (987, 1,401) | 1,110 (783, 1,399) | 1,087 (811, 1,570) | 0.5 | 0.6 |
| Magnesium.mg. | 299 (254, 339) | 361 (251, 475) | 437 (297, 608) | <0.001 | <0.001 |
| Zinc.mg. | 8.5 (6.5, 10.8) | 8.0 (5.0, 12.0) | 11.2 (6.6, 14.8) | 0.019 | 0.032 |
| Selenium.μg. | 37 (25, 48) | 23 (16, 37) | 22 (15, 34) | <0.001 | <0.001 |
| Iron.mg. | 9 (8, 12) | 11 (7, 14) | 13 (10, 20) | <0.001 | <0.001 |
| Calcium.mg. | 881 (674, 1,075) | 773 (554, 1,058) | 711 (555, 952) | 0.051 | 0.076 |
| Iodine.μg. | 73 (60, 87) | 64 (46, 69) | 59 (40, 82) | 0.015 | 0.028 |
| 1
Median (Q1, Q3) |
|||||
| 2
Kruskal-Wallis rank sum test |
|||||
| 3
False discovery rate correction for multiple testing |
|||||
Open code
food_int_adult_df <- food_int_adult$table_body %>%
as_tibble()3.2 Plots of nutrient intake
Preparation
Open code
## define color
colo <- c('#329243', '#ACE1A3', '#F9FFAF')
## prepare data
df <- dat_food %>%
mutate(Age_category2 = recode(Age_category,
`Ch > 3 yrs` = 'child_old',
`Ch < 3 yrs` = 'child_young')) %>%
mutate(super_group = interaction(GRP, Age_category2)) %>%
mutate(super_group = fct_relevel(
super_group,
'OM.child_young', 'VG.child_young', 'VN.child_young',
'OM.child_old', 'VG.child_old', 'VN.child_old',
'OM.adult', 'VG.adult', 'VN.adult')) %>%
mutate(GRP = fct_relevel(
GRP,
'VN', 'VG', 'OM')) %>%
mutate(Age_category = fct_relevel(
Age_category,
'Ch < 3 yrs', 'Ch > 3 yrs', 'adult'))
## define outcomes of interest
outcomes <- data.frame(
variable = df %>%
select(Calories.kcal.:Iodine.μg.) %>%
colnames())
outcomes <- outcomes %>%
mutate(
title = str_extract(variable, "^[^.]+"),
y_title = str_extract(variable, "(?<=\\.).*") %>%
str_replace_all("\\.", "/day")
)
outcomes$title[1] <- 'Energy'
outcomes$title[7] <- 'Saturate fats'
outcomes$y_title[7] <- 'g/day'Boxplot
Open code
## function to boxplot
boxplot_cond <- function(variable, y_title, title) {
clean_data <- df %>%
select(Age_category, GRP, super_group, variable) %>%
drop_na()
upper_limit <- max(clean_data[[variable]]) * 1.3
p <- ggboxplot(clean_data,
x = 'GRP',
y = variable,
fill = 'GRP',
tip.length = 0.15,
palette = colo,
outlier.shape = 1,
lwd = 0.25,
outlier.size = 0.8,
facet.by = 'Age_category',
title = title,
ylab = y_title) +
theme(
plot.title = element_text(size = 10),
axis.title = element_text(size = 8),
axis.text = element_text(size = 7),
axis.title.x = element_blank()
) +
coord_cartesian(ylim = c(NA, upper_limit))
return(p)
}
# Plot all outcomes
plots <- pmap(outcomes, boxplot_cond)
# Create a matrix of plots
plots_arranged <- ggarrange(plotlist = plots, ncol = 4, nrow = 4, common.legend = TRUE)
plots_arrangedOpen code
path <- paste0('gitignore/figures/plots_arranged.pdf')
if(file.exists(path) == FALSE){
ggsave(path,
plot = plots_arranged,
width = 13, height = 10,
device = cairo_pdf)
}
path <- paste0('gitignore/figures/plots_arranged.tiff')
if(file.exists(path) == FALSE){
tiff(path, width = 13, height = 10, units = 'in', res = 400)
grid.draw(plots_arranged)
dev.off()
}4 Reproducibility
Open code
sessionInfo()
## R version 4.4.3 (2025-02-28)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=cs_CZ.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=cs_CZ.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=cs_CZ.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Europe/Prague
## tzcode source: system (glibc)
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] mice_3.17.0 patchwork_1.2.0 ggrepel_0.9.5 robustlmm_3.3-1
## [5] gridExtra_2.3 pheatmap_1.0.12 performance_0.12.2 quantreg_5.98
## [9] SparseM_1.81 bayesplot_1.8.1 ggdist_3.3.2 kableExtra_1.4.0
## [13] lubridate_1.8.0 corrplot_0.92 arm_1.12-2 MASS_7.3-64
## [17] projpred_2.0.2 glmnet_4.1-8 boot_1.3-31 cowplot_1.1.1
## [21] pROC_1.18.0 mgcv_1.9-1 nlme_3.1-167 openxlsx_4.2.5
## [25] flextable_0.9.6 sjPlot_2.8.16 car_3.1-2 carData_3.0-5
## [29] gtsummary_2.0.2 emmeans_1.10.4 ggpubr_0.4.0 lme4_1.1-35.5
## [33] Matrix_1.7-0 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
## [37] purrr_1.0.2 readr_2.1.2 tidyr_1.3.1 tibble_3.2.1
## [41] ggplot2_3.5.1 tidyverse_1.3.1
##
## loaded via a namespace (and not attached):
## [1] splines_4.4.3 later_1.3.0 gamm4_0.2-6
## [4] cellranger_1.1.0 datawizard_0.12.2 rpart_4.1.24
## [7] reprex_2.0.1 lifecycle_1.0.4 rstatix_0.7.0
## [10] lattice_0.22-5 insight_0.20.2 backports_1.5.0
## [13] magrittr_2.0.3 sass_0.4.9 rmarkdown_2.27
## [16] yaml_2.3.5 httpuv_1.6.5 zip_2.2.0
## [19] askpass_1.1 DBI_1.1.2 minqa_1.2.4
## [22] RColorBrewer_1.1-2 multcomp_1.4-18 abind_1.4-5
## [25] rvest_1.0.2 nnet_7.3-20 TH.data_1.1-0
## [28] sandwich_3.0-1 gdtools_0.3.7 crul_1.5.0
## [31] cards_0.2.2 MatrixModels_0.5-3 commonmark_1.9.1
## [34] svglite_2.1.3 codetools_0.2-19 xml2_1.3.3
## [37] tidyselect_1.2.1 shape_1.4.6 farver_2.1.0
## [40] ggeffects_1.7.0 httpcode_0.3.0 base64enc_0.1-3
## [43] matrixStats_1.3.0 jsonlite_1.8.8 mitml_0.4-3
## [46] ellipsis_0.3.2 ggridges_0.5.3 survival_3.7-0
## [49] iterators_1.0.14 systemfonts_1.0.4 foreach_1.5.2
## [52] tools_4.4.3 ragg_1.2.1 Rcpp_1.0.13
## [55] glue_1.7.0 pan_1.6 xfun_0.46
## [58] distributional_0.4.0 loo_2.4.1 withr_3.0.1
## [61] fastmap_1.2.0 fansi_1.0.6 openssl_1.4.6
## [64] digest_0.6.37 R6_2.5.1 mime_0.12
## [67] estimability_1.5.1 textshaping_0.3.6 colorspace_2.0-2
## [70] markdown_1.13 utf8_1.2.4 generics_0.1.3
## [73] fontLiberation_0.1.0 data.table_1.15.4 robustbase_0.93-9
## [76] httr_1.4.2 htmlwidgets_1.6.4 pkgconfig_2.0.3
## [79] gtable_0.3.0 htmltools_0.5.8.1 fontBitstreamVera_0.1.1
## [82] scales_1.3.0 knitr_1.48 rstudioapi_0.16.0
## [85] tzdb_0.2.0 uuid_1.0-3 coda_0.19-4
## [88] curl_4.3.2 nloptr_2.0.0 zoo_1.8-9
## [91] sjlabelled_1.2.0 parallel_4.4.3 pillar_1.9.0
## [94] vctrs_0.6.5 promises_1.2.0.1 jomo_2.7-3
## [97] dbplyr_2.1.1 xtable_1.8-4 evaluate_1.0.0
## [100] fastGHQuad_1.0.1 mvtnorm_1.1-3 cli_3.6.3
## [103] compiler_4.4.3 rlang_1.1.4 crayon_1.5.0
## [106] rstantools_2.1.1 ggsignif_0.6.3 labeling_0.4.2
## [109] modelr_0.1.8 plyr_1.8.6 sjmisc_2.8.10
## [112] fs_1.6.4 stringi_1.7.6 viridisLite_0.4.0
## [115] assertthat_0.2.1 munsell_0.5.0 fontquiver_0.2.1
## [118] sjstats_0.19.0 hms_1.1.1 gfonts_0.2.0
## [121] shiny_1.9.1 haven_2.4.3 gt_0.11.0
## [124] broom_1.0.6 DEoptimR_1.0-10 readxl_1.3.1
## [127] officer_0.6.6